Ehanced protein expression in bacillus

ABSTRACT

The present invention provides cells that have been genetically manipulated to have an altered capacity to produce expressed proteins. In particular, the present invention relates to Gram-positive microorganisms, such as  Bacillus  species having enhanced expression of a protein of interest, wherein one or more chromosomal genes have been inactivated, and preferably wherein one or more chromosomal genes have been deleted from the  Bacillus  chromosome. In some further embodiments, one or more indigenous chromosomal regions have been deleted from a corresponding wild-type  Bacillus  host chromosome.

FIELD OF THE INVENTION

The present invention provides cells that have been geneticallymanipulated to have an altered capacity to produce expressed proteins.In particular, the present invention relates to Gram-positivemicroorganisms, such as Bacillus species having enhanced expression of aprotein of interest, wherein one or more chromosomal genes have beeninactivated, and preferably wherein one or more chromosomal genes havebeen deleted from the Bacillus chromosome. In some further embodiments,one or more indigenous chromosomal regions have been deleted from acorresponding wild-type Bacillus host chromosome.

BACKGROUND OF THE INVENTION

Genetic engineering has allowed the improvement of microorganisms usedas industrial bioreactors, cell factories and in food fermentations. Inparticular, Bacillus species produce and secrete a large number ofuseful proteins and metabolites (Zukowski, “Production of commerciallyvaluable products,” In: Doi and McGlouglin (eds.) Biology of Bacilli:Applications to Industry, Butterworth-Heinemann, Stoneham. Mass. pp311-337 [1992]). The most common Bacillus species used in industry areB. licheniformis, B. amyloliquefaciens and B. subtilis. Because of theirGRAS (generally recognized as safe) status, strains of these Bacillusspecies are natural candidates for the production of proteins utilizedin the food and pharmaceutical industries. Important production enzymesinclude α-amylases, neutral proteases, and alkaline (or serine)proteases. However, in spite of advances in the understanding ofproduction of proteins in Bacillus host cells, there remains a need formethods to increase expression of these proteins.

SUMMARY OF THE INVENTION

The present invention provides cells that have been geneticallymanipulated to have an altered capacity to produce expressed proteins.In particular, the present invention relates to Gram-positivemicroorganisms, such as Bacillus species having enhanced expression of aprotein of interest, wherein one or more chromosomal genes have beeninactivated, and preferably wherein one or more chromosomal genes havebeen deleted from the Bacillus chromosome. In some further embodiments,one or more indigenous chromosomal regions have been deleted from acorresponding wild-type Bacillus host chromosome. In some preferredembodiments, the present invention provides methods and compositions forthe improved expression and/or secretion of a protein of interest inBacillus.

In particularly preferred embodiments, the present invention providesmeans for improved expression and/or secretion of a protein of interestin Bacillus. More particularly, in these embodiments, the presentinvention involves inactivation of one or more chromosomal genes in aBacillus host strain, wherein the inactivated genes are not necessaryfor strain viability. One result of inactivating one or more of thechromosomal genes is the production of an altered Bacillus strain thatis able to express a higher level of a protein of interest over acorresponding non-altered Bacillus host strain.

Furthermore, in alternative embodiments, the present invention providesmeans for removing large regions of chromosomal DNA in a Bacillus hoststrain, wherein the deleted indigenous chromosomal region is notnecessary for strain viability. One result of removing one or moreindigenous chromosomal regions is the production of an altered Bacillusstrain that is able to express a higher level of a protein of interestover a corresponding unaltered Bacillus strain. In some preferredembodiments, the Bacillus host strain is a recombinant host straincomprising a polynucleotide encoding a protein of interest. In someparticularly preferred embodiments, the altered Bacillus strain is a B.subtilis strain. As explained in detail below, deleted indigenouschromosomal regions include, but are not limited to prophage regions,antimicrobial (e.g., antibiotic) regions, regulator regions,multi-contiguous single gene regions and operon regions.

In some embodiments, the present invention provides methods andcompositions for enhancing expression of a protein of interest from aBacillus cell. In some preferred embodiments, the methods compriseinactivating one or more chromosomal genes selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS trpA,trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA,fbp, rocA, ycgN, ycgM, rocF, and rocD in a Bacillus host strain toproduce an altered Bacillus strain; growing the altered Bacillus strainunder suitable growth conditions; and allowing a protein of interest tobe expressed in the altered Bacillus, wherein the expression of theprotein is enhanced, compared to the corresponding unaltered Bacillushost strain. In some embodiments, the protein of interest is ahomologous protein, while in other embodiments, the protein of interestis a heterologous protein. In some embodiments, more than one protein ofinterest is produced. In some preferred embodiments, the Bacillusspecies is a B. subtilis strain. In yet further embodiments,inactivation of a chromosomal gene comprises the deletion of a gene toproduce the altered Bacillus strain. In additional embodiments,inactivation of a chromosomal gene comprises insertional inactivation.In some preferred embodiments, the protein of interest is an enzyme. Insome embodiments, the protein of interest is selected from proteases,cellulases, amylases, carbohydrases, lipases, isomerases, transferases,kinases and phosphatases, while in other embodiments, the protein ofinterest is selected from the group consisting of antibodies, hormonesand growth factors.

In yet additional embodiments, the present invention provides alteredBacillus strains comprising the deletion of one or more chromosomalgenes selected from the group of sbo, slr, ybcO, csn, spoIISA, sigB,phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD,sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD. In someembodiments, the altered strain is a protease producing Bacillus strain.In an alternative embodiment, the altered Bacillus strain is asubtilisin producing strain. In yet other embodiments, the alteredBacillus strain further comprises a mutation in a gene selected from thegroup consisting of degU, degQ, degS, scoC4, spoIIE, and oppA.

In further embodiments, the present invention provides DNA constructscomprising an incoming sequence. In some embodiments, the incomingsequence includes a selective marker and a gene or gene fragmentselected from the group consisting of sbo, slr, ybcO, csn, spoIISA,sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl,alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD. Inalternative embodiments, the selective marker is located in between twofragments of the gene. In other embodiments, the incoming sequencecomprises a selective marker and a homology box, wherein the homologybox flanks the 5′ and/or 3′ end of the marker. In additionalembodiments, a host cell is transformed with the DNA construct. Infurther embodiments, the host cell is an E. coli or a Bacillus cell. Insome preferred embodiments, the DNA construct is chromosomallyintegrated into the host cell.

The present invention also provides methods for obtaining an alteredBacillus strain expressing a protein of interest which comprisestransforming a Bacillus host cell with the DNA construct of the present,wherein the DNA construct is integrated into the chromosome of theBacillus host cell; producing an altered Bacillus strain, wherein one ormore chromosomal genes have been inactivated; and growing the alteredBacillus strain under suitable growth conditions for the expression of aprotein of interest. In some embodiments, the protein of interest isselected from proteases, cellulases, amylases, carbohydrases, lipases,isomerases, transferases, kinases and phosphatases, while in otherembodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors. In yet additionalembodiments, the Bacillus host strain is selected from the groupconsisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. alkalophilus, B.coagulans, B. circulans, B. pumilus, B. thuringiensis, B. clausii, B.megaterium, and preferably, B. subtilis. In some embodiments, theBacillus host strain is a recombinant host. In yet additionalembodiments, the protein of interest is recovered. In furtherembodiments, the selective marker is excised from the altered Bacillus.

The present invention further provides methods for obtaining an alteredBacillus strain expressing a protein of interest. In some embodiments,the method comprises transforming a Bacillus host cell with a DNAconstruct comprising an incoming sequence wherein the incoming sequencecomprises a selective marker and a gene selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS,trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB,pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD, wherein the DNA constructis integrated into the chromosome of the Bacillus host cell and resultsin the deletion of one or more gene(s); obtaining an altered Bacillusstrain, and growing the altered Bacillus strain under suitable growthconditions for the expression of the protein of interest.

In some alternative embodiments, the present invention provides a DNAconstruct comprising an incoming sequence, wherein the incoming sequenceincludes a selective marker and a cssS gene, a cssS gene fragment or ahomologous sequence thereto. In some embodiments, the selective markeris located between two fragments of the gene. In alternativeembodiments, the incoming sequence comprises a selective marker and ahomology box wherein the homology box flanks the 5′ and/or 3′ end of themarker. In yet other embodiments, a host cell is transformed with theDNA construct. In additional embodiments, the host cell is an E. coli ora Bacillus cell. In still further embodiments, the DNA construct ischromosomally integrated into the host cell.

The present invention also provides methods for obtaining Bacillussubtilis strains that demonstrate enhanced protease production. In someembodiments, the methods comprise the steps of transforming a Bacillussubtilis host cell with a DNA construct according to the invention;allowing homologous recombination of the DNA construct and a homologousregion of the Bacillus chromosome wherein at least one of the followinggenes, sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS, trpA, trpB,trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp,rocA, ycgN, ycgM, rocF, and rocD, is deleted from the Bacilluschromosome; obtaining an altered Bacillus subtilis strain; and growingthe altered Bacillus strain under conditions suitable for the expressionof a protease. In some embodiments, the protease producing Bacillus is asubtilisin producing strain. In alternative embodiments, the protease isa heterologous protease. In additional embodiments, the proteaseproducing strain further includes a mutation in a gene selected from thegroup consisting of degU, degQ, degS, scoC4, spoIIE, and oppA. In someembodiments, the inactivation comprises the insertional inactivation ofthe gene.

The present invention further provides altered Bacillus subtilis strainscomprising a deletion of one or more chromosomal genes selected from thegroup consisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA,CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC,gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD, wherein the alteredBacillus subtilis strain is capable of expressing a protein of interest.In some embodiments, the protein of interest is an enzyme. In someadditional embodiments, the protein of interest is a heterologousprotein.

In some embodiments, the present invention provides altered Bacillusstrains comprising a deletion of one or more indigenous chromosomalregions or fragments thereof, wherein the indigenous chromosomal regionincludes about 0.5 to 500 kilobases (kb) and wherein the alteredBacillus strains have an enhanced level of expression of a protein ofinterest compared to the corresponding unaltered Bacillus strains whengrown under essentially the same growth conditions.

In yet additional embodiments, the present invention providesprotease-producing Bacillus strains which comprise at least one deletionof an indigenous chromosomal region selected from the group consistingof a PBSX region, a skin region, a prophage 7 region, a SPβ region, aprophage 1 region, a prophage 2 region, a prophage 3 region, a prophage4 region, a prophage 5 region, a prophage 6 region, a PPS region, a PKSregion, a yvfF-yveK region, a DHB region and fragments thereof.

In further embodiments, the present invention provides methods forenhancing the expression of a protein of interest in Bacilluscomprising: obtaining an altered Bacillus strain produced by introducinga DNA construct including a selective marker and an inactivatingchromosomal segment into a Bacillus host strain, wherein the DNAconstruct is integrated into the Bacillus chromosome resulting in thedeletion of an indigenous chromosomal region or fragment thereof fromthe Bacillus host cell; and growing the altered Bacillus strain undersuitable growth conditions, wherein expression of a protein of interestis greater in the altered Bacillus strain compared to the expression ofthe protein of interest is the corresponding unaltered Bacillus hostcell.

The present invention also provides methods for obtaining a protein ofinterest from a Bacillus strain comprising the steps of: transforming aBacillus host cell with a DNA construct which comprises a selectivemarker and an inactivating chromosomal segment, wherein the DNAconstruct is integrated into the chromosome of the Bacillus strain andresults in deletion of an indigenous chromosomal region or fragmentthereof to form an altered Bacillus strain; culturing the alteredBacillus strain under suitable growth conditions to allow the expressionof a protein of interest; and recovering the protein of interest.

The present invention also provides a means for the use of DNAmicroarray data to screen and/or identify beneficial mutations. In someparticularly preferred embodiments, these mutations involve genesselected from the group consisting of trpA, trpB, trpC, trpD, trpE,trpF, tdh/kbl rocA, ycgN, ycgM, rocF, and rocD. In some preferredembodiments, these beneficial mutations are based on transcriptomeevidence for the simultaneous expression of a given amino acidbiosynthetic pathway and biodegradative pathway, and/or evidence thatdeletion of the degradative pathway results in a better performingstrain and/or evidence that overexpression of the biosynthetic pathwayresults in a better performing strain. In additional embodiments, thepresent invention provides means for the use of DNA microarray data toprovide beneficial mutations. In some particularly preferredembodiments, these mutations involve genes selected from the groupconsisting of trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl rocA, ycgN,ycgM, rocF, and rocD, when the expression of mRNA from genes comprisingan amino acid biosynthetic pathway is not balanced and overexpression ofthe entire pathway provides a better performing strain than the parent(i.e., wild-type and/or originating) strain. Furthermore, the presentinvention provides means to improve production strains through theinactivation of gluconeogenic genes. In some of these preferredembodiments, the inactivated gluconeogenic genes are selected from thegroup consisting of pckA, gapB, and fbp.

The present invention provides methods for enhancing expression of aprotein of interest from Bacillus comprising the steps of obtaining analtered Bacillus strain capable of producing a protein of interest,wherein the altered Bacillus strain has at least one inactivatedchromosomal gene selected from the group consisting of sbo, slr, ybcO,csn, spoIISA, sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE,trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM,rocF, and rocD, and growing the altered Bacillus strain under conditionssuch that the protein of interest is expressed by the altered Bacillusstrain, wherein the expression of the protein of interest is enhanced,compared to the expression of the protein of interest in an unalteredBacillus host strain. In some embodiments, the protein of interest isselected from the group consisting of homologous proteins andheterologous proteins. In some embodiments, the protein of interest isselected from proteases, cellulases, amylases, carbohydrases, lipases,isomerases, transferases, kinases and phosphatases, while in otherembodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors. In someparticularly preferred embodiments, the protein of interest is aprotease. In additional embodiments, the altered Bacillus strain isobtained by deleting one or more chromosomal genes selected from thegroup consisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA,CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC,gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD.

The present invention also provides altered Bacillus strains obtainedusing the method described herein. In some preferred embodiments, thealtered Bacillus strains comprise a chromosomal deletion of one or moregenes selected from the group consisting of sbo, slr, ybcO, csn,spoIISA, sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF,tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, androcD. In some embodiments, more than one of these chromosomal genes havebeen deleted. In some particularly preferred embodiments, the alteredstrains are B. subtilis strains. In additional preferred embodiments,the altered Bacillus strains are protease producing strains. In someparticularly preferred embodiments, the protease is a subtilisin. In yetadditional is embodiments, the subtilisin is selected from the groupconsisting of subtilisin 168, subtilisin BPN′, subtilisin Carlsberg,subtilisin DY, subtilisin 147, subtilisin 309 and variants thereof. Inyet further embodiments, altered Bacillus strains further comprisemutation(s) in at least one gene selected from the group consisting ofdegU, degQ, degS, scoC4, spoIIE, and oppA. In some particularlypreferred embodiments, the altered Bacillus strains further comprise aheterologous protein of interest.

The present invention also provides DNA constructs comprising at leastone gene selected from the group consisting of sbo, slr, ybcO, csn,spoIISA, sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF,tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, androcD, gene fragments thereof, and homologous sequences thereto. In somepreferred embodiments, the DNA constructs comprise at least one nucleicacid sequence selected from the group consisting of SEQ ID NO: 1, SEQ IDNO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ IDNO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:39, SEQ ID NO:40, SEQ IDNO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:37, SEQ ID NO:25, SEQ ID NO:21, SEQ ID NO:50, SEQ ID NO:29, SEQ IDNO:23, SEQ ID NO:27, SEQ ID NO:19, SEQ ID NO:31, SEQ ID NO:48, SEQ IDNO:46, SEQ ID NO:35, and SEQ ID NO:33. In some embodiments, the DNAconstructs further comprise at least one polynucleotide sequenceencoding at least one protein of interest.

The present invention also provides plasmids comprising the DNAconstructs. In further embodiments, the present invention provides hostcells comprising the plasmids comprising the DNA constructs. In someembodiments, the host cells are selected from the group consisting ofBacillus cells and E. coli cells. In some preferred embodiments, thehost cell is B. subtilis. In some particularly preferred embodiments,the DNA construct is integrated into the chromosome of the host cell. Inalternative embodiments, the DNA construct comprises at least one genethat encodes at least one amino acid sequence selected from the groupconsisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8,SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO:18, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ IDNO:49, SEQ ID NO:51, SEQ ID NO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ IDNO:57, SEQ ID NO:30, SEQ ID NO:24, SEQ ID NO:28, SEQ ID NO:20, SEQ IDNO:32, SEQ ID NO:55, SEQ ID NO:53, SEQ ID NO:36, and SEQ ID NO:34. Inadditional embodiments, the DNA constructs further comprise at least oneselective marker, wherein the selective marker is flanked on each sideby a fragment of the gene or homologous gene sequence thereto.

The present invention also provides DNA constructs comprising anincoming sequence, wherein the incoming sequence comprises a nucleicacid encoding a protein of interest, and a selective marker flanked oneach side with a homology box, wherein the homology box includes nucleicacid sequences having 80 to 100% sequence identity to the sequenceimmediately flanking the coding regions of at least one gene selectedfrom the group consisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC,rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD,prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD. In someembodiments, the DNA constructs further comprise at least one nucleicacids which flanks the coding sequence of the gene. The presentinvention also provides plasmids comprising the DNA constructs. Infurther embodiments, the present invention provides host cellscomprising the plasmids comprising the DNA constructs. In someembodiments, the host cells are selected from the group consisting ofBacillus cells and E. coli cells. In some preferred embodiments, thehost cell is B. subtilis. In some particularly preferred embodiments,the DNA construct is integrated into the chromosome of the host cell. Inadditional preferred embodiments, the selective marker has been excisedfrom the host cell chromosome.

The present invention further provides methods for obtaining an alteredBacillus strain with enhanced protease production comprising:transforming a Bacillus host cell with at least one DNA construct of thepresent invention, wherein the protein of interest in the DNA constructis a protease, and wherein the DNA construct is integrated into thechromosome of the Bacillus host cell under conditions such that at leastone gene is inactivated to produce an altered Bacillus strain; andgrowing the altered Bacillus strain under conditions such that enhancedprotease production is obtained. In some particularly preferredembodiments, the method further comprises recovering the protease. Inalternative preferred embodiments, at least one inactivated gene isdeleted from the chromosome of the altered Bacillus strain. The presentinvention also provides altered Bacillus strains produced using themethods described herein. In some embodiments, the Bacillus host strainis selected from the group consisting of B. licheniformis, B. lentus, B.subtilis, B. amyloliquefaciens B. brevis, B. stearothermophilus, B.alkalophilus, B. coagulans, B. circulans, B. pumilus, B. lautus, B.clausii, B. megaterium, and B. thuringiensis. In some preferredembodiments, the Bacillus host cell is B. subtilis.

The present invention also provides methods for enhancing expression ofa protease in an altered Bacillus comprising: transforming a Bacillushost cell with a DNA construct of the present invention; allowinghomologous recombination of the DNA construct and a region of thechromosome of the Bacillus host cell, wherein at least one gene of thechromosome of the Bacillus host cell is inactivated, to produce analtered Bacillus strain; and growing the altered Bacillus strain underconditions suitable for the expression of the protease, wherein theproduction of the protease is greater in the altered Bacillus subtilisstrain compared to the Bacillus subtilis host prior to transformation.In some preferred embodiments, the protease is subtilisin. In additionalembodiments, the protease is a recombinant protease. In yet furtherembodiments, inactivation is achieved by deletion of at least one gene.In still further embodiments, inactivation is by insertionalinactivation of at least one gene. The present invention also providesaltered Bacillus strains obtained using the methods described herein. Insome embodiments, altered Bacillus strain comprises at least oneinactivated gene selected from the group consisting of sbo, slr, ybcO,csn, spoIISA, sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE,trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM,rocF, and rocD. In some preferred embodiments, the inactivated gene hasbeen inactivated by deletion. In additional embodiments, the alteredBacillus strains further comprise at least one mutation in a geneselected from the group consisting of degU, degS, degQ, scoC4, spoIIE,and oppA. In some preferred embodiments, the mutation is degU(Hy)32. Instill further embodiments, the strain is a recombinant proteaseproducing strain. In some preferred embodiments, the altered Bacillusstrains are selected from the group consisting of B. licheniformis, B.lentus, B. subtilis, B. amyloliquefaciens B. brevis, B.stearothermophilus, B. alkalophilus, B. coagulans, B. circulans, B.pumilus, B. lautus, B. clausii, B. megaterium, and B. thuringiensis.

The present invention also provides altered Bacillus strains comprisinga deletion of one or more indigenous chromosomal regions or fragmentsthereof, wherein the indigenous chromosomal region includes about 0.5 to500 kb, and wherein the altered Bacillus strain has an enhanced level ofexpression of a protein of interest compared to a correspondingunaltered Bacillus strain when the altered and unaltered Bacillusstrains are grown under essentially the same growth conditions. Inpreferred embodiments, the altered Bacillus strain is selected from thegroup consisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. alkalophilus, B.coagulans, B. circulans, B. pumilus, B. lautus, B. clausii, B.megaterium, and B. thuringiensis. In some preferred embodiments, thealtered Bacillus strain is selected from the group consisting of B.subtilis, B. licheniformis, and B. amyloliquefaciens. In someparticularly preferred embodiments, the altered Bacillus strain is a B.subtilis strain. In yet further embodiments, the indigenous chromosomalregion is selected from the group consisting of a PBSX region, a skinregion, a prophage 7 region, a SPβ region, a prophage 1 region, aprophage 2 region, a prophage 4 region, a prophage 3 region, a prophage4 region, a prophage 5 region, a prophage 6, region, a PPS region, a PKSregion, a YVFF-YVEK region, a DHB region and fragments thereof. In somepreferred embodiments, two indigenous chromosomal regions or fragmentsthereof have been deleted. In some embodiments, the protein of interestis selected from proteases, cellulases, amylases, carbohydrases,lipases, isomerases, transferases, kinases and phosphatases, while inother embodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors. In yet additionalembodiments, the protein of interest is a protease. In some preferredembodiments, the protease is a subtilisin. In some particularlypreferred embodiments, the subtilisin is selected from the groupconsisting of subtilisin 168, subtilisin BPN′, subtilisin Carlsberg,subtilisin DY, subtilisin 147 and subtilisin 309 and variants thereof.In further preferred embodiments, the Bacillus host is a recombinantstrain. In some particularly preferred embodiments, the altered Bacillusstrains further comprise at least one mutation in a gene selected fromthe group consisting of degU, degQ, degS, sco4, spoIIE and oppA. In somepreferred embodiments, the mutation is degU(Hy)32.

The present invention further provides protease producing Bacillusstrains comprising a deletion of an indigenous chromosomal regionselected from the group consisting of a PBSX region, a skin region, aprophage 7 region, a SPβ region, a prophage 1 region, a prophage 2region, a prophage 3 region, a prophage 4 region, a prophage 5 region, aprophage 6 region, a PPS region, a PKS region, a YVFF-YVEK region, a DHBregion and fragments thereof. In some preferred embodiments, theprotease is a subtilisin. In some embodiments, the protease is aheterologous protease. In some preferred embodiments, the alteredBacillus strain is selected from the group consisting of B.licheniformis, B. lentus, B. subtilis, B. amyloliquefaciens B. brevis,B. stearothermophilus, B. alkalophilus, B. coagulans, B. circulans, B.pumilus, B. lautus, B. clausii, B. megaterium, and B. thuringiensis. Inadditional embodiments, the Bacillus strain is a B. subtilis strain.

The present invention also provides methods for enhancing the expressionof a protein of interest in Bacillus comprising: introducing a DNAconstruct including a selective marker and an inactivating chromosomalsegment into a Bacillus host strain, wherein the DNA construct isintegrated into the chromosome of the Bacillus host strain, resulting inthe deletion of an indigenous chromosomal region or fragment thereoffrom the Bacillus host cell to produce an altered Bacillus strain; andgrowing the altered Bacillus strain under suitable conditions, whereinexpression of a protein of interest is greater in the altered Bacillusstrain compared to the expression of the protein of interest in aBacillus host cell that has not been altered. In some preferredembodiments, the methods further comprise the step of recovering theprotein of interest. In some embodiments, the methods further comprisethe step of excising the selective marker from the altered Bacillusstrain. In additional embodiments, the indigenous chromosomal region isselected from the group of regions consisting of PBSX, skin, prophage 7,SPβ, prophage 1, prophage 2, prophage 3, prophage 4, prophage 5,prophage 6, PPS, PKS, YVFF-YVEK, DHB and fragments thereof. In furtherembodiments, the altered Bacillus strain comprises deletion of at leasttwo indigenous chromosomal regions. In some preferred embodiments, theprotein of interest is an enzyme. In some embodiments, the protein ofinterest is selected from proteases, cellulases, amylases,carbohydrases, lipases, isomerases, transferases, kinases andphosphatases, while in other embodiments, the protein of interest isselected from the group consisting of antibodies, hormones and growthfactors. In some embodiments, the Bacillus host strain is selected fromthe group consisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. clausii, B.alkalophilus, B. coagulans, B. circulans, B. pumilus and B.thuringiensis. The present invention also provides altered Bacillusstrains produced using the methods described herein.

The present invention also provides methods for obtaining a protein ofinterest from a Bacillus strain comprising: transforming a Bacillus hostcell with a DNA construct comprising a selective marker and aninactivating chromosomal segment, wherein the DNA construct isintegrated into the chromosome of the Bacillus strain resulting indeletion of an indigenous chromosomal region or fragment thereof, toproduce an altered Bacillus strain, culturing the altered Bacillusstrain under suitable growth conditions to allow the expression of aprotein of interest, and recovering the protein of interest. In somepreferred embodiments, the protein of interest is an enzyme. In someparticularly preferred embodiments, the Bacillus host comprises aheterologous gene encoding a protein of interest. In additionalembodiments, the Bacillus host cell is selected from the groupconsisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. clausii, B.alkalophilus, B. coagulans, B. circulans, B. pumilus and B.thuringiensis. In some preferred embodiments, the indigenous chromosomalregion is selected from the group of regions consisting of PBSX, skin,prophage 7, SPβ, prophage 1, prophage 2, prophage 3, prophage 4,prophage 5, prophage 6, PPS, PKS, YVFF-YVEK, DHB and fragments thereof.In some particularly preferred embodiments the altered Bacillus strainsfurther comprise at least one mutation in a gene selected from the groupconsisting of degU, degQ, degS, sco4, spoIIE and oppA. In someembodiments, the protein of interest is an enzyme selected from thegroup consisting of proteases, cellulases, amylases, carbohydrases,lipases, isomerases, transferases, kinases, and phosphatases. In someparticularly preferred embodiments, the enzyme is a protease. In somepreferred embodiments, the protein of interest is an enzyme. In otherembodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors.

The present invention further provides methods for enhancing theexpression of a protein of interest in Bacillus comprising: obtainingnucleic acid from at least one Bacillus cell; performing transcriptomeDNA array analysis on the nucleic acid from said Bacillus cell toidentify at least one gene of interest; modifying at least one gene ofinterest to produce a DNA construct; introducing the DNA construct intoa Bacillus host cell to produce an altered Bacillus strain, wherein thealtered Bacillus strain is capable of producing a protein of interest,under conditions such that expression of the protein of interest isenhanced as compared to the expression of the protein of interest in aBacillus that has not been altered. In some embodiments, the protein ofinterest is associated with at least one biochemical pathway selectedfrom the group consisting of amino acid biosynthetic pathways andbiodegradative pathways. In some embodiments, the methods involvedisabling at least one biodegradative pathway. In some embodiments, thebiodegradative pathway is disabled due to the transcription of the geneof interest. However, it is not intended that the present invention belimited to these pathways, as it is contemplated that the methods willfind use in the modification of other biochemical pathways within cellssuch that enhanced expression of a protein of interest results. In someparticularly preferred embodiments, the Bacillus host comprises aheterologous gene encoding a protein of interest. In additionalembodiments, the Bacillus host cell is selected from the groupconsisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. clausii, B.alkalophilus, B. coagulans, B. circulans, B. pumilus and B.thuringiensis. In some embodiments, the protein of interest is anenzyme. In some preferred embodiments, the protein of interest isselected from proteases, cellulases, amylases, carbohydrases, lipases,isomerases, transferases, kinases and phosphatases, while in otherembodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors.

The present invention further provides methods for enhancing theexpression of a protein of interest in Bacillus, comprising: obtainingnucleic acid containing at least one gene of interest from at least oneBacillus cell; fragmenting said nucleic acid; amplifying said fragmentsto produce a pool of amplified fragments comprising said at least onegene of interest; ligating said amplified fragments to produce a DNAconstruct; directly transforming said DNA construct into a Bacillus hostcell to produce an altered Bacillus strain; culturing said alteredBacillus strain under conditions such that expression of said protein ofinterest is enhanced as compared to the expression of said protein ofinterest in a Bacillus that has not been altered. In some preferredembodiments, said amplifying comprises using the polymerase chainreaction. In some embodiments, the altered Bacillus strain comprisesmodified gene selected from the group consisting of prpC, sigD andtdh/kbl. In some particularly preferred embodiments, the Bacillus hostcomprises a heterologous gene encoding a protein of interest. Inadditional embodiments, the Bacillus host cell is selected from thegroup consisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. clausii, B.alkalophilus, B. coagulans, B. circulans, B. pumilus and B.thuringiensis. In some embodiments, the protein of interest is anenzyme. In some preferred embodiments, the protein of interest isselected from proteases, cellulases, amylases, carbohydrases, lipases,isomerases, transferases, kinases and phosphatases, while in otherembodiments, the protein of interest is selected from the groupconsisting of antibodies, hormones and growth factors.

The present invention further provides isolated nucleic acids comprisingthe sequences set forth in nucleic acid sequences selected from thegroup consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO:7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ IDNO:39, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ IDNO:48, SEQ ID NO:50, SEQ ID NO:37, SEQ ID NO:25, SEQ ID NO:21, SEQ IDNO:50, SEQ ID NO:23, SEQ ID NO:27, SEQ ID NO:19, SEQ ID NO:31, SEQ IDNO:48, SEQ ID NO:46, SEQ ID NO:35, and SEQ ID NO:33.

The present invention also provides isolated nucleic acid sequencesencoding amino acids, wherein the amino acids are selected from thegroup consisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ IDNO:51, SEQ ID NO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ ID NO:57, SEQ IDNO:24, SEQ ID NO:28, SEQ ID NO:20, SEQ ID NO:32, SEQ ID NO:55, SEQ IDNO:53, SEQ ID NO:36, and SEQ ID NO:34.

The present invention further provides isolated amino acid sequences,wherein the amino acid sequences are selected from the group consistingof SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO:10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO:41, SEQ IDNO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ IDNO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ ID NO:57, SEQ ID NO:24, SEQ IDNO:28, SEQ ID NO:20, SEQ ID NO:32, SEQ ID NO:55, SEQ ID NO:53, SEQ IDNO:36, and SEQ ID NO:34.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1, Panels A and B illustrate a general schematic diagram of onemethod (“Method 1” See, Example 1) provided by the present invention. Inthis method, flanking regions of a gene and/or an indigenous chromosomalregion are amplified out of a wild-type Bacillus chromosome, cut withrestriction enzymes (including at least BamHI) and ligated into pJM102.The construct is cloned through E. coli and the plasmid is isolated,linearized with BamHI and ligated to an antimicrobial marker withcomplementary ends. After cloning again in E. coli, a liquid culture isgrown and used to isolate plasmid DNA for use in transforming a Bacillushost strain (preferably, a competent Bacillus host strain).

FIG. 2 illustrates the location of primers used in the construction of aDNA cassette according to some embodiments of the present invention. Thediagram provides an explanation of the primer naming system used herein.Primers 1 and 4 are used for checking the presence of the deletion.These primers are referred to as “DeletionX-UF-chk” and“DeletionX-UR-chk-del.” DeletionX-UF-chk is also used in a PCR reactionwith a reverse primer inside the antimicrobial marker (Primer 11: calledfor example PBSX-UR-chk-Del) for a positive check of the cassette'spresence in the chromosome. Primers 2 and 6 are used to amplify theupstream flanking region. These primers are referred to as“DeletionX-UF” and “DeletionX-UR,” and contain engineered restrictionsites at the black vertical bars. Primers 5 and 8 are used to amplifythe downstream flanking region. These primers are referred to as“DeletionX-DF” and “DeletionX-DR.” These primers may either containengineered BamHI sites for ligation and cloning, or 25 base pair tailshomologous to an appropriate part of the Bacillus subtilis chromosomefor use in PCR fusion. In some embodiments, primers 3 and 7 are used tofuse the cassette together in the case of those cassettes created by PCRfusion, while in other embodiments, they are used to check for thepresence of the insert. These primers are referred to as“DeletionX-UF-nested” and “DeletionX-DR-nested.” In some embodiments,the sequence corresponding to an “antibiotic marker” is a Spc resistancemarker and the region to be deleted is the CssS gene.

FIG. 3 is a general schematic diagram of one method (“Method 2”; SeeExample 2) of the present invention. Flanking regions are engineered toinclude 25 bp of sequence complementary to a selective marker sequence.The selective marker sequence also includes 25 bp tails that complementDNA of one flanking region. Primers near the ends of the flankingregions are used to amplify all three templates in a single reactiontube, thereby creating a fusion fragment. This fusion fragment or DNAconstruct is directly transformed into a competent Bacillus host strain.

FIG. 4 provides an electrophoresis gel of Bacillus DHB deletion clones.Lanes 1 and 2 depict two strains carrying the DHB deletion amplifiedwith primers 1 and 11, and illustrate a 1.2 kb band amplified fromupstream of the inactivating chromosomal segments into the phleomycinmarker. Lane 3 depicts the wild-type control for this reaction. Onlynon-specific amplification is observed. Lanes 4 and 5 depict the DHBdeleted strains amplified with primers 9 and 12. This 2 kb bandamplifies through the antibiotic region to below the downstream sectionof the inactivated chromosomal segment. Lane 6 is the negative controlfor this reaction and a band is not illustrated. Lanes 7 and 8 depictthe deletion strains amplified with primers 1 and 4 and the illustrationconfirms that the DHB region is missing. Lane 9 is the wild-typecontrol.

FIG. 5 illustrates gel electrophoresis of two clones of a productionstrain of Bacillus subtilis (wild-type) wherein slr is replaced with aphleomycin (phleo) marker which results in a deletion of the slr gene.Lanes 1 and 2 represent the clones amplified with primers at locations 1and 11. Lane 3 is the wild-type chromosomal DNA amplified with the sameprimers. A 1.2 kb band is observed for the insert. Lanes 4 and 5represent the clones amplified with primers at locations 9 and 12. Lane6 is the wild-type chromosomal DNA amplified with the same primers.Correct transformants include a 2 kb band. Lanes 7 and 8 represent theclones amplified with primers at locations 2 and 4. Lane 9 is thewild-type chromosomal DNA amplified with the same primers. No band isobserved for the deletion strains, but a band around 1 kb is observed inthe wild-type. Reference is made to FIG. 2 for an explanation of primerlocations.

FIG. 6 provides an electrophoresis gel of a clone of a production strainof Bacillus subtilis (wild-type) wherein cssS is inactivated by theintegration of a spc marker into the chromosome. Lane 1 is a controlwithout the integration and is approximately 1.5 kb smaller.

FIG. 7 provides a bar graph showing improved subtilisin secretionmeasured from shake flask cultures with Bacillus subtilis wild-typestrain (unaltered) and corresponding altered Bacillus subtilis strainshaving various deletions. Protease activity (g/L) was measured after 17,24 and 40 hours or was measured at 24 and 40 hours.

FIG. 8 provides a bar graph showing improved protease secretion asmeasured from shake flask cultures in Bacillus subtilis wild-type strain(unaltered) and corresponding altered deletion strains (−sbo) and(−slr). Protease activity (g/L) was measured after 17, 24 and 40 hours.

DESCRIPTION OF THE INVENTION

The present invention provides cells that have been geneticallymanipulated to have an altered capacity to produce expressed proteins.In particular, the present invention relates to Gram-positivemicroorganisms, such as Bacillus species having enhanced expression of aprotein of interest, wherein one or more chromosomal genes have beeninactivated or otherwise modified. In some preferred embodiments, one ormore chromosomal genes have been deleted from the Bacillus chromosome.In some further embodiments, one or more indigenous chromosomal regionshave been deleted from a corresponding wild-type Bacillus hostchromosome.

Definitions

All patents and publications, including all sequences disclosed withinsuch patents and publications, referred to herein are expresslyincorporated by reference. Unless defined otherwise herein, alltechnical and scientific terms used herein have the same meaning ascommonly understood by one of ordinary skill in the art to which thisinvention belongs (See e.g., Singleton et al., DICTIONARY OFMICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, NewYork [1994]; and Hale and Marham, THE HARPER COLLINS DICTIONARY OFBIOLOGY, Harper Perennial, NY [1991], both of which provide one of skillwith a general dictionary of many of the terms used herein). Althoughany methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention,the preferred methods and materials are described. Numeric ranges areinclusive of the numbers defining the range. As used herein and in theappended claims, the singular “a”, “an” and “the” includes the pluralreference unless the context clearly dictates otherwise. Thus, forexample, reference to a “host cell” includes a plurality of such hostcells.

Unless otherwise indicated, nucleic acids are written left to right in5′ to 3′ orientation; amino acid sequences are written left to right inamino to carboxy orientation, respectively. The headings provided hereinare not limitations of the various aspects or embodiments of theinvention that can be had by reference to the specification as a whole.Accordingly, the terms defined immediately below are more fully definedby reference to the Specification as a whole.

As used herein, “host cell” refers to a cell that has the capacity toact as a host or expression vehicle for a newly introduced DNA sequence.In preferred embodiments of the present invention, the host cells areBacillus sp. or E. coli cells.

As used herein, “the genus Bacillus” includes all species within thegenus “Bacillus,” as known to those of skill in the art, including butnot limited to B. subtilis, B. licheniformis, B. lentus, B. brevis, B.stearothermophilus, B. alkalophilus, B. amyloliquefaciens, B. clausii,B. halodurans, B. megaterium, B. coagulans, B. circulans, B. lautus, andB. thuringiensis. It is recognized that the genus Bacillus continues toundergo taxonomical reorganization. Thus, it is intended that the genusinclude species that have been reclassified, including but not limitedto such organisms as B. stearothermophilus, which is now named“Geobacillus stearothermophilus.” The production of resistant endosporesin the presence of oxygen is considered the defining feature of thegenus Bacillus, although this characteristic also applies to therecently named Alicyclobacillus, Amphibacillus, Aneurinibacillus,Anoxybacillus, Brevibacillus, Filobacillus, Gracilibacillus,Halobacillus, Paenibacillus, Salibacillus, Thermobacillus, Ureibacillus,and Virgibacillus.

As used herein, “nucleic acid” refers to a nucleotide or polynucleotidesequence, and fragments or portions thereof, as well as to DNA, cDNA,and RNA of genomic or synthetic origin which may be double-stranded orsingle-stranded, whether representing the sense or antisense strand. Itwill be understood that as a result of the degeneracy of the geneticcode, a multitude of nucleotide sequences may encode a given protein.

As used herein the term “gene” means a chromosomal segment of DNAinvolved in producing a polypeptide chain that may or may not includeregions preceding and following the coding regions (e.g. 5′ untranslated(5′ UTR) or leader sequences and 3′ untranslated (3′ UTR) or trailersequences, as well as intervening sequence (introns) between individualcoding segments (exons)).

In some embodiments, the gene encodes therapeutically significantproteins or peptides, such as growth factors, cytokines, ligands,receptors and inhibitors, as well as vaccines and antibodies. The genemay encode commercially important industrial proteins or peptides, suchas enzymes (e.g., proteases, carbohydrases such as amylases andglucoamylases, cellulases, oxidases and lipases). However, it is notintended that the present invention be limited to any particular enzymeor protein. In some embodiments, the gene of interest is anaturally-occurring gene, while in other embodiments, it is a mutatedgene or a synthetic gene.

As used herein, the term “vector” refers to any nucleic acid that can bereplicated in cells and can carry new genes or DNA segments into cells.Thus, the term refers to a nucleic acid construct designed for transferbetween different host cells. An “expression vector” refers to a vectorthat has the ability to incorporate and express heterologous DNAfragments in a foreign cell. Many prokaryotic and eukaryotic expressionvectors are commercially available. Selection of appropriate expressionvectors is within the knowledge of those having skill in the art.

As used herein, the terms “DNA construct,” “expression cassette,” and“expression vector,” refer to a nucleic acid construct generatedrecombinantly or synthetically, with a series of specified nucleic acidelements that permit transcription of a particular nucleic acid in atarget cell (i.e., these are vectors or vector elements, as describedabove). The recombinant expression cassette can be incorporated into aplasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleicacid fragment. Typically, the recombinant expression cassette portion ofan expression vector includes, among other sequences, a nucleic acidsequence to be transcribed and a promoter. In some embodiments, DNAconstructs also include a series of specified nucleic acid elements thatpermit transcription of a particular nucleic acid in a target cell. Inone embodiment, a DNA construct of the invention comprises a selectivemarker and an inactivating chromosomal segment as defined herein.

As used herein, “transforming DNA,” “transforming sequence,” and “DNAconstruct” refer to DNA that is used to introduce sequences into a hostcell or organism. Transforming DNA is DNA used to introduce sequencesinto a host cell or organism. The DNA may be generated in vitro by PCRor any other suitable techniques. In some preferred embodiments, thetransforming DNA comprises an incoming sequence, while in otherpreferred embodiments it further comprise an incoming sequence flankedby homology boxes. In yet a further embodiment, the transforming DNAcomprises other non-homologous sequences, added to the ends (i.e.,stuffer sequences or flanks). The ends can be closed such that thetransforming DNA forms a closed circle, such as, for example, insertioninto a vector.

As used herein, the term “plasmid” refers to a circular double-stranded(ds) DNA construct used as a cloning vector, and which forms anextrachromosomal self-replicating genetic element in many bacteria andsome eukaryotes. In some embodiments, plasmids become incorporated intothe genome of the host cell.

As used herein, the terms “isolated” and “purified” refer to a nucleicacid or amino acid (or other component) that is removed from at leastone component with which it is naturally associated.

As used herein, the term “enhanced expression” is broadly construed toinclude enhanced production of a protein of interest. Enhancedexpression is that expression above the normal level of expression inthe corresponding host strain that has not been altered according to theteachings herein but has been grown under essentially the same growthconditions.

In some preferred embodiments, “enhancement” is achieved by anymodification that results in an increase in a desired property. Forexample, in some particularly preferred embodiments, the presentinvention provides means for enhancing protein production, such that theenhanced strains produced a greater quantity and/or quality of a proteinof interest than the parental strain (e.g., the wild-type and/ororiginating strain).

As used herein the term “expression” refers to a process by which apolypeptide is produced based on the nucleic acid sequence of a gene.The process includes both transcription and translation.

As used herein in the context of introducing a nucleic acid sequenceinto a cell, the term “introduced” refers to any method suitable fortransferring the nucleic acid sequence into the cell. Such methods forintroduction include but are not limited to protoplast fusion,transfection, transformation, conjugation, and transduction (See e.g.,Ferrari et al., “Genetics,” in Hardwood et al, (eds.), Bacillus, PlenumPublishing Corp., pages 57-72, [1989]).

As used herein, the terms “transformed” and “stably transformed” refersto a cell that has a non-native (heterologous) polynucleotide sequenceintegrated into its genome or as an episomal plasmid that is maintainedfor at least two generations.

As used herein “an incoming sequence” refers to a DNA sequence that isintroduced into the Bacillus chromosome. In some preferred embodiments,the incoming sequence is part of a DNA construct. In preferredembodiments, the incoming sequence encodes one or more proteins ofinterest. In some embodiments, the incoming sequence comprises asequence that may or may not already be present in the genome of thecell to be transformed (i.e., it may be either a homologous orheterologous sequence). In some embodiments, the incoming sequenceencodes one or more proteins of interest, a gene, and/or a mutated ormodified gene. In alternative embodiments, the incoming sequence encodesa functional wild-type gene or operon, a functional mutant gene oroperon, or a non-functional gene or operon. In some embodiments, thenon-functional sequence may be inserted into a gene to disrupt functionof the gene. In some embodiments, the incoming sequence encodes one ormore functional wild-type genes, while in other embodiments, theincoming sequence encodes one or more functional mutant genes, and inyet additional embodiments, the incoming sequence encodes one or morenon-functional genes. In another embodiment, the incoming sequenceencodes a sequence that is already present in the chromosome of the hostcell to be transformed. In a preferred embodiment, the incoming sequencecomprises a gene selected from the group consisting of sbo, slr, ybcO,csn, spoIISA, phrC, sigB, rapA, CssS, trpA, trpB, trpC, trpD, trpE,trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM,rocF, and rocD, and fragments thereof. In yet another embodiment, theincoming sequence includes a selective marker. In a further embodimentthe incoming sequence includes two homology boxes.

In some embodiments, the incoming sequence encodes at least oneheterologous protein including, but not limited to hormones, enzymes,and growth factors. In another embodiment, the enzyme includes, but isnot limited to hydrolases, such as protease, esterase, lipase, phenoloxidase, permease, amylase, pullulanase, cellulase, glucose isomerase,laccase and protein disulfide isomerase.

As used herein, “homology box” refers to a nucleic acid sequence, whichis homologous to a sequence in the Bacillus chromosome. Morespecifically, a homology box is an upstream or downstream region havingbetween about 80 and 100% sequence identity, between about 90 and 100%sequence identity, or between about 95 and 100% sequence identity withthe immediate flanking coding region of a gene or part of a gene to beinactivated according to the invention. These sequences direct where inthe Bacillus chromosome a DNA construct is integrated and directs whatpart of the Bacillus chromosome is replaced by the incoming sequence.While not meant to limit the invention, a homology box may include aboutbetween 1 base pair (bp) to 200 kilobases (kb). Preferably, a homologybox includes about between 1 bp and 10.0 kb; between 1 bp and 5.0 kb;between 1 bp and 2.5 kb; between 1 bp and 1.0 kb, and between 0.25 kband 2.5 kb. A homology box may also include about 10.0 kb, 5.0 kb, 2.5kb, 2.0 kb, 1.5 kb, 1.0 kb, 0.5 kb, 0.25 kb and 0.1 kb. In someembodiments, the 5′ and 3′ ends of a selective marker are flanked by ahomology box wherein the homology box comprises nucleic acid sequencesimmediately flanking the coding region of the gene.

As used herein, the term “selectable marker-encoding nucleotidesequence” refers to a nucleotide sequence which is capable of expressionin the host cells and where expression of the selectable marker confersto cells containing the expressed gene the ability to grow in thepresence of a corresponding selective agent or lack of an essentialnutrient.

As used herein, the terms “selectable marker” and “selective marker”refer to a nucleic acid (e.g., a gene) capable of expression in hostcell which allows for ease of selection of those hosts containing thevector. Examples of such selectable markers include but are not limitedto antimicrobials. Thus, the term “selectable marker” refers to genesthat provide an indication that a host cell has taken up an incoming DNAof interest or some other reaction has occurred. Typically, selectablemarkers are genes that confer antimicrobial resistance or a metabolicadvantage on the host cell to allow cells containing the exogenous DNAto be distinguished from cells that have not received any exogenoussequence during the transformation. A “residing selectable marker” isone that is located on the chromosome of the microorganism to betransformed. A residing selectable marker encodes a gene that isdifferent from the selectable marker on the transforming DNA construct.Selective markers are well known to those of skill in the art. Asindicated above, preferably the marker is an antimicrobial resistantmarker (e.g., amp^(R); phleo^(R); spec^(R); kan^(R); ery^(R); tet^(R);cmp^(R); and neo^(R); See e.g., Guerot-Fleury, Gene, 167:335-337 [1995];Palmeros et al., Gene 247:255-264 [2000]; and Trieu-Cuot et al., Gene,23:331-341 [1983]). In some particularly preferred embodiments, thepresent invention provides a chloramphenicol resistance gene (e.g., thegene present on pC194, as well as the resistance gene present in theBacillus licheniformis genome). This resistance gene is particularlyuseful in the present invention, as well as in embodiments involvingchromosomal amplification of chromosomally integrated cassettes andintegrative plasmids (See e.g., Albertini and Galizzi, Bacteriol.,162:1203-1211 [1985]; and Stahl and Ferrari, J. Bacteriol., 158:411-418[1984]). The DNA sequence of this naturally-occurring chloramphenicolresistance gene is shown below: (SEQ ID NO:58)ATGAATTTTCAAACAATCGAGCTTGACACATGGTATAGAAAATCTTATTTTGACCATTACATGAAGGAAGCGAAATGTTCTTTCAGCATCACGGCAAACGTCAATGTGACAAATTTGCTCGCCGTGCTCAAGAAAAAGAAGCTCAAGCTGTATCCGGCTTTTATTTATATCGTATCAAGGGTCATTCATTCGCGCCCTGAGTTTAGAACAACGTTTGATGACAAAGGAAGCTGGGTTATTGGGAACAAATGCATCCGTGCTATGCGATTTTTCATCAGGACGACCAAACGTTTTCCGCCCTCTGGACGGAATACTCAGACGATTTTTCGCAGTTTTATCATCAATATCTTCTGGACGCCGAGCGCTTTGGAGACAAAAGGGGCCTTTGGGCTAAGCCGGACATCCCGCCCAATACGTTTTCAGTTTCTTCTATTCCATGGGTGCGCTTTTCAACATTCAATTTAAACCTTGATAACAGCGAACACTTGCTGCCGATTATTACAAACGGGAAATACTTTTCAGAAGGCAGGGAAACATTTTTGCCCGTTTCCTGCAAGTTCACCATGCAGTGTGTGACGGCTATCATGCCGGCGCTTTTAT AA.

The deduced amino acid sequence of this chloramphenicol resistanceprotein is: (SEQ ID NO:59)MNFQTIELDTWYRKSYFDHYMKEAKCSFSITANVNVTNLLAVLKKKKLKLYPAFIYIVSRVIHSRPEFRTTFDDKGQLGYWEQMHPCYAIFHQDDQTFSALWTEYSDDFSQFYHQYLLDAERFGDKRGLWAKPDIPPNTFSVSSIPWVRFSTFNLNLDNSEHLLPIITNGKYFSEGRETFLPVSCKFTMQCVTAIM PALL.

Other markers useful in accordance with the invention include, but arenot limited to auxotrophic markers, such as tryptophan; and detectionmarkers, such as β-galactosidase.

As used herein, the term “promoter” refers to a nucleic acid sequencethat functions to direct transcription of a downstream gene. Inpreferred embodiments, the promoter is appropriate to the host cell inwhich the target gene is being expressed. The promoter, together withother transcriptional and translational regulatory nucleic acidsequences (also termed “control sequences”) is necessary to express agiven gene. In general, the transcriptional and translational regulatorysequences include, but are not limited to, promoter sequences, ribosomalbinding sites, transcriptional start and stop sequences, translationalstart and stop sequences, and enhancer or activator sequences.

A nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNAencoding a secretory leader (i.e., a signal peptide), is operably linkedto DNA for a polypeptide if it is expressed as a preprotein thatparticipates in the secretion of the polypeptide; a promoter or enhanceris operably linked to a coding sequence if it affects the transcriptionof the sequence; or a ribosome binding site is operably linked to acoding sequence if it is positioned so as to facilitate translation.Generally, “operably linked” means that the DNA sequences being linkedare contiguous, and, in the case of a secretory leader, contiguous andin reading phase. However, enhancers do not have to be contiguous.Linking is accomplished by ligation at convenient restriction sites. Ifsuch sites do not exist, the synthetic oligonucleotide adaptors orlinkers are used in accordance with conventional practice.

The term “inactivation” includes any method that prevents the functionalexpression of one or more of the sbo, slr, ybcO, csn, spoIISA, sigB,phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD,sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocDchromosomal genes, wherein the gene or gene product is unable to exertits known function. Inactivation or enhancement occurs via any suitablemeans, including deletions, substitutions (e.g., mutations),interruptions, and/or insertions in the nucleic acid gene sequence. Inone embodiment, the expression product of an inactivated gene is atruncated protein with a corresponding change in the biological activityof the protein. In some embodiments, the change in biological activityis an increase in activity, while in preferred embodiments, the changeis results in the loss of biological activity. In some embodiments, analtered Bacillus strain comprises inactivation of one or more genes thatresults preferably in stable and non-reverting inactivation.

In some preferred embodiments, inactivation is achieved by deletion. Insome preferred embodiments, the gene is deleted by homologousrecombination. For example, in some embodiments when sbo is the gene tobe deleted, a DNA construct comprising an incoming sequence having aselective marker flanked on each side by a homology box is used. Thehomology box comprises nucleotide sequences homologous to nucleic acidsflanking regions of the chromosomal sbo gene. The DNA construct alignswith the homologous sequences of the Bacillus host chromosome and in adouble crossover event the sbo gene is excised out of the hostchromosome.

As used herein, “deletion” of a gene refers to deletion of the entirecoding sequence, deletion of part of the coding sequence, or deletion ofthe coding sequence including flanking regions. The deletion may bepartial as long as the sequences left in the chromosome provides thedesired biological activity of the gene. The flanking regions of thecoding sequence may include from about 1 bp to about 500 bp at the 5′and 3′ ends. The flanking region may be larger than 500 bp but willpreferably not include other genes in the region which may beinactivated or deleted according to the invention. The end result isthat the deleted gene is effectively non-functional. In simple terms, a“deletion” is defined as a change in either nucleotide or amino acidsequence in which one or more nucleotides or amino acid residues,respectively, have been removed (i.e., are absent). Thus, a “deletionmutant” has fewer nucleotides or amino acids than the respectivewild-type organism.

In still another embodiment of the present invention, deletion of a geneactive at an inappropriate time as determined by DNA array analysis(e.g., transcriptome analysis, as described herein) provides enhancedexpression of a product protein. In some preferred embodiments, deletionof one or more of genes selected from the group consisting of pckA,gapB, fbp, and/or alsD, provides an improved strain for the improvedefficiency of feed utilization. As used herein, “transcriptome analysis”refers to the analysis of gene transcription.

In another embodiment of the present invention, a gene is considered tobe “optimized” by the deletion of a regulatory sequence in which thisdeletion results in increased expression of a desired product. In somepreferred embodiments of the present invention, the tryptophan operon(i.e., comprising genes trpA trpB, trpC, trpD, trpE, trpF) is optimizedby the deletion of the DNA sequence coding for the TRAP binding RNAsequence (See, Yang, et. al., J. Mol. Biol., 270:696-710 [1997]). Thisdeletion is contemplated to increase expression of the desired productfrom the host strain.

In another preferred embodiment, inactivation is by insertion. Forexample, in some embodiments, when sbo is the gene to be inactivated, aDNA construct comprises an incoming sequence having the sbo geneinterrupted by a selective marker. The selective marker will be flankedon each side by sections of the sbo coding sequence. The DNA constructaligns with essentially identical sequences of the sbo gene in the hostchromosome and in a double crossover event the sbo gene is inactivatedby the insertion of the selective marker. In simple terms, an“insertion” or “addition” is a change in a nucleotide or amino acidsequence which has resulted in the addition of one or more nucleotidesor amino acid residues, respectively, as compared to the naturallyoccurring sequence.

In another embodiment, activation is by insertion in a single crossoverevent with a plasmid as the vector. For example, a sbo chromosomal geneis aligned with a plasmid comprising the gene or part of the gene codingsequence and a selective marker. In some embodiments, the selectivemarker is located within the gene coding sequence or on a part of theplasmid separate from the gene. The vector is integrated into theBacillus chromosome, and the gene is inactivated by the insertion of thevector in the coding sequence.

In alternative embodiments, inactivation results due to mutation of thegene. Methods of mutating genes are well known in the art and includebut are not limited to site-directed mutation, generation of randommutations, and gapped-duplex approaches (See e.g., U.S. Pat. No.4,760,025; Moring et al., Biotech. 2:646 [1984]; and Kramer et al.,Nucleic Acids Res., 12:9441 [1984]).

As used herein, a “substitution” results from the replacement of one ormore nucleotides or amino acids by different nucleotides or amino acids,respectively.

As used herein, “homologous genes” refers to a pair of genes fromdifferent, but usually related species, which correspond to each otherand which are identical or very similar to each other. The termencompasses genes that are separated by speciation (i.e., thedevelopment of new species) (e.g., orthologous genes), as well as genesthat have been separated by genetic duplication (e.g., paralogousgenes).

As used herein, “ortholog” and “orthologous genes” refer to genes indifferent species that have evolved from a common ancestral gene (i.e.,a homologous gene) by speciation. Typically, orthologs retain the samefunction in during the course of evolution. Identification of orthologsfinds use in the reliable prediction of gene function in newly sequencedgenomes.

As used herein, “paralog” and “paralogous genes” refer to genes that arerelated by duplication within a genome. While orthologs retain the samefunction through the course of evolution, paralogs evolve new functions,even though some functions are often related to the original one.Examples of paralogous genes include, but are not limited to genesencoding trypsin, chymotrypsin, elastase, and thrombin, which are allserine proteinases and occur together within the same species.

As used herein, “homology” refers to sequence similarity or identity,with identity being preferred. This homology is determined usingstandard techniques known in the art (See e.g., Smith and Waterman, Adv.Appl. Math., 2:482 [1981]; Needleman and Wunsch, J. Mol. Biol., 48:443[1970]; Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444 [1988];programs such as GAP, BESTFIT, FASTA, and TFASTA in the WisconsinGenetics Software Package (Genetics Computer Group, Madison, Wis.); andDevereux et al., Nucl. Acid Res., 12:387-395 [1984]).

As used herein, an “analogous sequence” is one wherein the function ofthe gene is essentially the same as the gene designated from Bacillussubtilis strain 168. Additionally, analogous genes include at least 60%,65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% sequenceidentity with the sequence of the Bacillus subtilis strain 168 gene.Alternately, analogous sequences have an alignment of between 70 to 100%of the genes found in the B. subtilis 168 region and/or have at leastbetween 5-10 genes found in the region aligned with the genes in the B.subtilis 168 chromosome. In additional embodiments more than one of theabove properties applies to the sequence. Analogous sequences aredetermined by known methods of sequence alignment. A commonly usedalignment method is BLAST, although as indicated above and below, thereare other methods that also find use in aligning sequences.

One example of a useful algorithm is PILEUP. PILEUP creates a multiplesequence alignment from a group of related sequences using progressive,pairwise alignments. It can also plot a tree showing the clusteringrelationships used to create the alignment. PILEUP uses a simplificationof the progressive alignment method of Feng and Doolittle (Feng andDoolittle, J. Mol. Evol., 35:351-360 [1987]). The method is similar tothat described by Higgins and Sharp (Higgins and Sharp, CABIOS 5:151-153[1989]). Useful PILEUP parameters including a default gap weight of3.00, a default gap length weight of 0.10, and weighted end gaps.

Another example of a useful algorithm is the BLAST algorithm, describedby Altschul et al., (Altschul et al., J. Mol. Biol., 215:403-410,[1990]; and Karlin et al., Proc. Natl. Acad. Sci. USA 90:5873-5787[1993]). A particularly useful BLAST program is the WU-BLAST-2 program(See, Altschul et al., Meth. Enzymol., 266:460-480 [1996]). WU-BLAST-2uses several search parameters, most of which are set to the defaultvalues. The adjustable parameters are set with the following values:overlap span=1, overlap fraction=0.125, word threshold (T)=11. The HSP Sand HSP S2 parameters are dynamic values and are established by theprogram itself depending upon the composition of the particular sequenceand composition of the particular database against which the sequence ofinterest is being searched. However, the values may be adjusted toincrease sensitivity. A % amino acid sequence identity value isdetermined by the number of matching identical residues divided by thetotal number of residues of the “longer” sequence in the aligned region.The “longer” sequence is the one having the most actual residues in thealigned region (gaps introduced by WU-Blast-2 to maximize the alignmentscore are ignored).

Thus, “percent (%) nucleic acid sequence identity” is defined as thepercentage of nucleotide residues in a candidate sequence that areidentical with the nucleotide residues of the sequence shown in thenucleic acid figures. A preferred method utilizes the BLASTN module ofWU-BLAST-2 set to the default parameters, with overlap span and overlapfraction set to 1 and 0.125, respectively.

The alignment may include the introduction of gaps in the sequences tobe aligned. In addition, for sequences which contain either more orfewer nucleosides than those of the nucleic acid figures, it isunderstood that the percentage of homology will be determined based onthe number of homologous nucleosides in relation to the total number ofnucleosides. Thus, for example, homology of sequences shorter than thoseof the sequences identified herein and as discussed below, will bedetermined using the number of nucleosides in the shorter sequence.

As used herein, the term “hybridization” refers to the process by whicha strand of nucleic acid joins with a complementary strand through basepairing, as known in the art.

A nucleic acid sequence is considered to be “selectively hybridizable”to a reference nucleic acid sequence if the two sequences specificallyhybridize to one another under moderate to high stringency hybridizationand wash conditions. Hybridization conditions are based on the meltingtemperature (Tm) of the nucleic acid binding complex or probe. Forexample, “maximum stringency” typically occurs at about Tm-5° C. (5°below the Tm of the probe); “high stringency” at about 5-10° C. belowthe Tm; “intermediate stringency” at about 10-20° C. below the Tm of theprobe; and “low stringency” at about 20-25° C. below the Tm.Functionally, maximum stringency conditions may be used to identifysequences having strict identity or near-strict identity with thehybridization probe; while an intermediate or low stringencyhybridization can be used to identify or detect polynucleotide sequencehomologs.

Moderate and high stringency hybridization conditions are well known inthe art. An example of high stringency conditions includes hybridizationat about 42° C. in 50% formamide, 5×SSC, 5× Denhardt's solution, 0.5%SDS and 100 μg/ml denatured carrier DNA followed by washing two times in2×SSC and 0.5% SDS at room temperature and two additional times in0.1×SSC and 0.5% SDS at 42° C. An example of moderate stringentconditions include an overnight incubation at 37° C. in a solutioncomprising 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate),50 mM sodium phosphate (pH 7.6), 5× Denhardt's solution, 10% dextransulfate and 20 mg/ml denaturated sheared salmon sperm DNA, followed bywashing the filters in 1×SSC at about 37-50° C. Those of skill in theart know how to adjust the temperature, ionic strength, etc. asnecessary to accommodate factors such as probe length and the like.

As used herein, “recombinant” includes reference to a cell or vector,that has been modified by the introduction of a heterologous nucleicacid sequence or that the cell is derived from a cell so modified. Thus,for example, recombinant cells express genes that are not found inidentical form within the native (non-recombinant) form of the cell orexpress native genes that are otherwise abnormally expressed, underexpressed or not expressed at all as a result of deliberate humanintervention. “Recombination, “recombining,” or generating a“recombined” nucleic acid is generally the assembly of two or morenucleic acid fragments wherein the assembly gives rise to a chimericgene.

In a preferred embodiment, mutant DNA sequences are generated with sitesaturation mutagenesis in at least one codon. In another preferredembodiment, site saturation mutagenesis is performed for two or morecodons. In a further embodiment, mutant DNA sequences have more than40%, more than 45%, more than 50%, more than 55%, more than 60%, morethan 65%, more than 70%, more than 75%, more than 80%, more than 85%,more than 90%, more than 95%, or more than 98% homology with thewild-type sequence. In alternative embodiments, mutant DNA is generatedin vivo using any known mutagenic procedure such as, for example,radiation, nitrosoguanidine and the like. The desired DNA sequence isthen isolated and used in the methods provided herein.

In an alternative embodiment, the transforming DNA sequence compriseshomology boxes without the presence of an incoming sequence. In thisembodiment, it is desired to delete the endogenous DNA sequence betweenthe two homology boxes. Furthermore, in some embodiments, thetransforming sequences are wild-type, while in other embodiments, theyare mutant or modified sequences. In addition, in some embodiments, thetransforming sequences are homologous, while in other embodiments, theyare heterologous.

As used herein, the term “target sequence” refers to a DNA sequence inthe host cell that encodes the sequence where it is desired for theincoming sequence to be inserted into the host cell genome. In someembodiments, the target sequence encodes a functional wild-type gene oroperon, while in other embodiments the target sequence encodes afunctional mutant gene or operon, or a nonfunctional gene or operon.

As used herein, a “flanking sequence” refers to any sequence that iseither upstream or downstream of the sequence being discussed (e.g., forgenes A-B-C, gene B is flanked by the A and C gene sequences). In apreferred embodiment, the incoming sequence is flanked by a homology boxon each side. In another embodiment, the incoming sequence and thehomology boxes comprise a unit that is flanked by stuffer sequence oneach side. In some embodiments, a flanking sequence is present on only asingle side (either 3′ or 5′), but in preferred embodiments, it is oneach side of the sequence being flanked. The sequence of each homologybox is homologous to a sequence in the Bacillus chromosome. Thesesequences direct where in the Bacillus chromosome the new construct getsintegrated and what part of the Bacillus chromosome will be replaced bythe incoming sequence. In a preferred embodiment, the 5′ and 3′ ends ofa selective marker are flanked by a polynucleotide sequence comprising asection of the inactivating chromosomal segment. In some embodiments, aflanking sequence is present on only a single side (either 3′ or 5′),while in preferred embodiments, it is present on each side of thesequence being flanked.

As used herein, the term “stuffer sequence” refers to any extra DNA thatflanks homology boxes (typically vector sequences). However, the termencompasses any non-homologous DNA sequence. Not to be limited by anytheory, a stuffer sequence provides a noncritical target for a cell toinitiate DNA uptake.

As used herein, the term “library of mutants” refers to a population ofcells which are identical in most of their genome but include differenthomologues of one or more genes. Such libraries find use for example, inmethods to identify genes or operons with improved traits.

As used herein, the terms “hypercompetent” and “super competent” meanthat greater than 1% of a cell population is transformable withchromosomal DNA (e.g., Bacillus DNA). Alternatively, the terms are usedin reference to cell populations in which greater than 10% of a cellpopulation is transformable with a self-replicating plasmid (e.g., aBacillus plasmid). Preferably, the super competent cells are transformedat a rate greater than observed for the wild-type or parental cellpopulation. Super competent and hypercompetent are used interchangeablyherein.

As used herein, the terms “amplification” and “gene amplification” referto a process by which specific DNA sequences are disproportionatelyreplicated such that the amplified gene becomes present in a higher copynumber than was initially present in the genome. In some embodiments,selection of cells by growth in the presence of a drug (e.g., aninhibitor of an inhibitable enzyme) results in the amplification ofeither the endogenous gene encoding the gene product required for growthin the presence of the drug or by amplification of exogenous (i.e.,input) sequences encoding this gene product, or both.

“Amplification” is a special case of nucleic acid replication involvingtemplate specificity. It is to be contrasted with non-specific templatereplication (i.e., replication that is template-dependent but notdependent on a specific template). Template specificity is heredistinguished from fidelity of replication (i.e., synthesis of theproper polynucleotide sequence) and nucleotide (ribo- or deoxyribo-)specificity. Template specificity is frequently described in terms of“target” specificity. Target sequences are “targets” in the sense thatthey are sought to be sorted out from other nucleic acid. Amplificationtechniques have been designed primarily for this sorting out.

As used herein, the term “co-amplification” refers to the introductioninto a single cell of an amplifiable marker in conjunction with othergene sequences (i.e., comprising one or more non-selectable genes suchas those contained within an expression vector) and the application ofappropriate selective pressure such that the cell amplifies both theamplifiable marker and the other, non-selectable gene sequences. Theamplifiable marker may be physically linked to the other gene sequencesor alternatively two separate pieces of DNA, one containing theamplifiable marker and the other containing the non-selectable marker,may be introduced into the same cell.

As used herein, the terms “amplifiable marker,” “amplifiable gene,” and“amplification vector” refer to a gene or a vector encoding a gene whichpermits the amplification of that gene under appropriate growthconditions.

“Template specificity” is achieved in most amplification techniques bythe choice of enzyme. Amplification enzymes are enzymes that, underconditions they are used, will process only specific sequences ofnucleic acid in a heterogeneous mixture of nucleic acid. For example, inthe case of Qβ replicase, MDV-1 RNA is the specific template for thereplicase (See e.g., Kacian et al., Proc. Natl. Acad. Sci. USA 69:3038[1972]). Other nucleic acids are not replicated by this amplificationenzyme. Similarly, in the case of T7 RNA polymerase, this amplificationenzyme has a stringent specificity for its own promoters (See,Chamberlin et al., Nature 228:227 [1970]). In the case of T4 DNA ligase,the enzyme will not ligate the two oligonucleotides or polynucleotides,where there is a mismatch between the oligonucleotide or polynucleotidesubstrate and the template at the ligation junction (See, Wu andWallace, Genomics 4:560 [1989]). Finally, Taq and Pfu polymerases, byvirtue of their ability to function at high temperature, are found todisplay high specificity for the sequences bounded and thus defined bythe primers; the high temperature results in thermodynamic conditionsthat favor primer hybridization with the target sequences and nothybridization with non-target sequences.

As used herein, the term “amplifiable nucleic acid” refers to nucleicacids which may be amplified by any amplification method. It iscontemplated that “amplifiable nucleic acid” will usually comprise“sample template.”

As used herein, the term “sample template” refers to nucleic acidoriginating from a sample which is analyzed for the presence of “target”(defined below). In contrast, “background template” is used in referenceto nucleic acid other than sample template which may or may not bepresent in a sample. Background template is most often inadvertent. Itmay be the result of carryover, or it may be due to the presence ofnucleic acid contaminants sought to be purified away from the sample.For example, nucleic acids from organisms other than those to bedetected may be present as background in a test sample.

As used herein, the term “primer” refers to an oligonucleotide, whetheroccurring naturally as in a purified restriction digest or producedsynthetically, which is capable of acting as a point of initiation ofsynthesis when placed under conditions in which synthesis of a primerextension product which is complementary to a nucleic acid strand isinduced, (i.e., in the presence of nucleotides and an inducing agentsuch as DNA polymerase and at a suitable temperature and pH). The primeris preferably single stranded for maximum efficiency in amplification,but may alternatively be double stranded. If double stranded, the primeris first treated to separate its strands before being used to prepareextension products. Preferably, the primer is anoligodeoxyribonucleotide. The primer must be sufficiently long to primethe synthesis of extension products in the presence of the inducingagent. The exact lengths of the primers will depend on many factors,including temperature, source of primer and the use of the method.

As used herein, the term “probe” refers to an oligonucleotide (i.e., asequence of nucleotides), whether occurring naturally as in a purifiedrestriction digest or produced synthetically, recombinantly or by PCRamplification, which is capable of hybridizing to anotheroligonucleotide of interest. A probe may be single-stranded ordouble-stranded. Probes are useful in the detection, identification andisolation of particular gene sequences. It is contemplated that anyprobe used in the present invention will be labeled with any “reportermolecule,” so that is detectable in any detection system, including, butnot limited to enzyme (e.g., ELISA, as well as enzyme-basedhistochemical assays), fluorescent, radioactive, and luminescentsystems. It is not intended that the present invention be limited to anyparticular detection system or label.

As used herein, the term “target,” when used in reference to thepolymerase chain reaction, refers to the region of nucleic acid boundedby the primers used for polymerase chain reaction. Thus, the “target” issought to be sorted out from other nucleic acid sequences. A “segment”is defined as a region of nucleic acid within the target sequence.

As used herein, the term “polymerase chain reaction” (“PCR”) refers tothe methods of U.S. Pat. Nos. 4,683,195 4,683,202, and 4,965,188, herebyincorporated by reference, which include methods for increasing theconcentration of a segment of a target sequence in a mixture of genomicDNA without cloning or purification. This process for amplifying thetarget sequence consists of introducing a large excess of twooligonucleotide primers to the DNA mixture containing the desired targetsequence, followed by a precise sequence of thermal cycling in thepresence of a DNA polymerase. The two primers are complementary to theirrespective strands of the double stranded target sequence. To effectamplification, the mixture is denatured and the primers then annealed totheir complementary sequences within the target molecule. Followingannealing, the primers are extended with a polymerase so as to form anew pair of complementary strands. The steps of denaturation, primerannealing and polymerase extension can be repeated many times (i.e.,denaturation, annealing and extension constitute one “cycle”; there canbe numerous “cycles”) to obtain a high concentration of an amplifiedsegment of the desired target sequence. The length of the amplifiedsegment of the desired target sequence is determined by the relativepositions of the primers with respect to each other, and therefore, thislength is a controllable parameter. By virtue of the repeating aspect ofthe process, the method is referred to as the “polymerase chainreaction” (hereinafter “PCR”). Because the desired amplified segments ofthe target sequence become the predominant sequences (in terms ofconcentration) in the mixture, they are said to be “PCR amplified”.

As used herein, the term “amplification reagents” refers to thosereagents (deoxyribonucleotide triphosphates, buffer, etc.), needed foramplification except for primers, nucleic acid template and theamplification enzyme. Typically, amplification reagents along with otherreaction components are placed and contained in a reaction vessel (testtube, microwell, etc.).

With PCR, it is possible to amplify a single copy of a specific targetsequence in genomic DNA to a level detectable by several differentmethodologies (e.g., hybridization with a labeled probe; incorporationof biotinylated primers followed by avidin-enzyme conjugate detection;incorporation of ³²P-labeled deoxynucleotide triphosphates, such as dCTPor dATP, into the amplified segment). In addition to genomic DNA, anyoligonucleotide or polynucleotide sequence can be amplified with theappropriate set of primer molecules. In particular, the amplifiedsegments created by the PCR process itself are, themselves, efficienttemplates for subsequent PCR amplifications.

As used herein, the terms “PCR product,” “PCR fragment,” and“amplification product” refer to the resultant mixture of compoundsafter two or more cycles of the PCR steps of denaturation, annealing andextension are complete. These terms encompass the case where there hasbeen amplification of one or more segments of one or more targetsequences.

As used herein, the term “RT-PCR” refers to the replication andamplification of RNA sequences. In this method, reverse transcription iscoupled to PCR, most often using a one enzyme procedure in which athermostable polymerase is employed, as described in U.S. Pat. No.5,322,770, herein incorporated by reference. In RT-PCR, the RNA templateis converted to cDNA due to the reverse transcriptase activity of thepolymerase, and then amplified using the polymerizing activity of thepolymerase (i.e., as in other PCR methods).

As used herein, the terms “restriction endonucleases” and “restrictionenzymes” refer to bacterial enzymes, each of which cut double-strandedDNA at or near a specific nucleotide sequence.

A “restriction site” refers to a nucleotide sequence recognized andcleaved by a given restriction endonuclease and is frequently the sitefor insertion of DNA fragments. In certain embodiments of the inventionrestriction sites are engineered into the selective marker and into 5′and 3′ ends of the DNA construct.

As used herein “an inactivating chromosomal segment” comprises twosections. Each section comprises polynucleotides that are homologouswith the upstream or downstream genomic chromosomal DNA that immediatelyflanks an indigenous chromosome region as defined herein. “Immediatelyflanks” means the nucleotides comprising the inactivating chromosomalsegment do not include the nucleotides defining the indigenouschromosomal region. The inactivating chromosomal segment directs wherein the Bacillus chromosome the DNA construct gets integrated and whatpart of the Bacillus chromosome will be replaced.

As used herein, “indigenous chromosomal region” and “a fragment of anindigenous chromosomal region” refer to a segment of the Bacilluschromosome which is deleted from a Bacillus host cell in someembodiments of the present invention. In general, the terms “segment,”“region,” “section,” and “element” are used interchangeably herein. Insome embodiments, deleted segments include one or more genes with knownfunctions, while in other embodiments, deleted segments include one ormore genes with unknown functions, and in other embodiments, the deletedsegments include a combination of genes with known and unknownfunctions. In some embodiments, indigenous chromosomal regions orfragments thereof include as many as 200 genes or more.

In some embodiments, an indigenous chromosomal region or fragmentthereof has a necessary function under certain conditions, but theregion is not necessary for Bacillus strain viability under laboratoryconditions. Preferred laboratory conditions include but are not limitedto conditions such as growth in a fermenter, in a shake flask on platedmedia, etc., at standard temperatures and atmospheric conditions (e.g.,aerobic).

An indigenous chromosomal region or fragment thereof may encompass arange of about 0.5 kb to 500 kb; about 1.0 kb to 500 kb; about 5 kb to500 kb; about 10 kb to 500 kb; about 10 kb to 200 kb; about 10 kb to 100kb; about 10 kb to 50 kb; about 100 kb to 500 kb; and about 200 kb to500 kb of the Bacillus chromosome. In another aspect, when an indigenouschromosomal region or fragment thereof has been deleted, the chromosomeof the altered Bacillus strain may include 99%, 98%, 97%, 96%, 95%, 94%,93%, 92%, 91%, 90%, 85%, 80%, 75% or 70% of the corresponding unalteredBacillus host chromosome. Preferably, the chromosome of an alteredBacillus strain according to the invention will include about 99 to 90%;99 to 92%; and 98 to 94% of the corresponding unaltered Bacillus hoststrain chromosome genome.

As used herein, “strain viability” refers to reproductive viability. Thedeletion of an indigenous chromosomal region or fragment thereof, doesnot deleteriously affect division and survival of the altered Bacillusstrain under laboratory conditions.

As used herein, “altered Bacillus strain” refers to a geneticallyengineered Bacillus sp. wherein a protein of interest has an enhancedlevel of expression and/or production as compared to the expressionand/or production of the same protein of interest in a correspondingunaltered Bacillus host strain grown under essentially the same growthconditions. In some embodiments, the enhanced level of expressionresults from the inactivation of one or more chromosomal genes. In oneembodiment, the enhanced level of expression results from the deletionof one or more chromosomal genes. In some embodiments, the alteredBacillus strains are genetically engineered Bacillus sp. having one ormore deleted indigenous chromosomal regions or fragments thereof,wherein a protein of interest has an enhanced level of expression orproduction, as compared to a corresponding unaltered Bacillus hoststrain grown under essentially the same growth conditions. In analternative embodiment, the enhanced level of expression results fromthe insertional inactivation of one or more chromosomal genes. In somealternate embodiments, enhanced level of expression results due toincreased activation or an otherwise optimized gene. In some preferredembodiments, the inactivated genes are selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, phrC, sigB, rapA, CssS,trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB,pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD.

In certain embodiments, the altered Bacillus strain comprise twoinactivated genes, while in other embodiments, there are threeinactivated genes, four inactivated genes, five inactivated genes, sixinactivated genes, or more. Thus, it is not intended that the number ofinactivated genes be limited to an particular number of genes. In someembodiments, the inactivated genes are contiguous to each another, whilein other embodiments, they are located in separate regions of theBacillus chromosome. In some embodiments, an inactivated chromosomalgene has a necessary function under certain conditions, but the gene isnot necessary for Bacillus strain viability under laboratory conditions.Preferred laboratory conditions include but are not limited toconditions such as growth in a fermenter, in a shake flask, platedmedia, etc., suitable for the growth of the microorganism.

As used herein, a “corresponding unaltered Bacillus strain” is the hoststrain (e.g., the originating and/or wild-type strain) from which theindigenous chromosomal region or fragment thereof is deleted or modifiedand from which the altered strain is derived.

As used herein, the term “chromosomal integration” refers to the processwhereby the incoming sequence is introduced into the chromosome of ahost cell (e.g., Bacillus). The homologous regions of the transformingDNA align with homologous regions of the chromosome. Subsequently, thesequence between the homology boxes is replaced by the incoming sequencein a double crossover (i.e., homologous recombination). In someembodiments of the present invention, homologous sections of aninactivating chromosomal segment of a DNA construct align with theflanking homologous regions of the indigenous chromosomal region of theBacillus chromosome. Subsequently, the indigenous chromosomal region isdeleted by the DNA construct in a double crossover (i.e., homologousrecombination).

“Homologous recombination” means the exchange of DNA fragments betweentwo DNA molecules or paired chromosomes at the site of identical ornearly identical nucleotide sequences. In a preferred embodiment,chromosomal integration is homologous recombination.

“Homologous sequences” as used herein means a nucleic acid orpolypeptide sequence having 100%, 99%, 98%, 97%, 96%, 95%, 94%, 93%,92%, 91%, 90%, 88%, 85%, 80%, 75%, or 70% sequence identity to anothernucleic acid or polypeptide sequence when optimally aligned forcomparison. In some embodiments, homologous sequences have between 85%and 100% sequence identity, while in other embodiments there is between90% and 100% sequence identity, and in more preferred embodiments, thereis 95% and 100% sequence identity.

As used herein “amino acid” refers to peptide or protein sequences orportions thereof. The terms “protein”, “peptide” and “polypeptide” areused interchangeably.

As used herein, “protein of interest” and “polypeptide of interest”refer to a protein/polypeptide that is desired and/or being assessed. Insome embodiments, the protein of interest is intracellular, while inother embodiments, it is a secreted polypeptide. Particularly preferredpolypeptides include enzymes, including, but not limited to thoseselected from amylolytic enzymes, proteolytic enzymes, cellulyticenzymes, oxidoreductase enzymes and plant cell-wall degrading enzymes.More particularly, these enzyme include, but are not limited toamylases, proteases, xylanases, lipases, laccases, phenol oxidases,oxidases, cutinases, cellulases, hemicellulases, esterases,perioxidases, catalases, glucose oxidases, phytases, pectinases,glucosidases, isomerases, transferases, galactosidases and chitinases.In some particularly preferred embodiments of the present invention, thepolypeptide of interest is a protease. In some embodiments, the proteinof interest is a secreted polypeptide which is fused to a signal peptide(i.e., an amino-terminal extension on a protein to be secreted). Nearlyall secreted proteins use an amino-terminal protein extension whichplays a crucial role in the targeting to and translocation of precursorproteins across the membrane. This extension is proteolytically removedby a signal peptidase during or immediately following membrane transfer.

In some embodiments of the present invention, the polypeptide ofinterest is selected from hormones, antibodies, growth factors,receptors, etc. Hormones encompassed by the present invention includebut are not limited to, follicle-stimulating hormone, luteinizinghormone, corticotropin-releasing factor, somatostatin, gonadotropinhormone, vasopressin, oxytocin, erythropoietin, insulin and the like.Growth factors include, but are not limited to platelet-derived growthfactor, insulin-like growth factors, epidermal growth factor, nervegrowth factor, fibroblast growth factor, transforming growth factors,cytokines, such as interleukins (e.g., IL-1 through IL-13), interferons,colony stimulating factors, and the like. Antibodies include but are notlimited to immunoglobulins obtained directly from any species from whichit is desirable to produce antibodies. In addition, the presentinvention encompasses modified antibodies. Polyclonal and monoclonalantibodies are also encompassed by the present invention. Inparticularly preferred embodiments, the antibodies are human antibodies.

As used herein, the term “heterologous protein” refers to a protein orpolypeptide that does not naturally occur in the host cell. Examples ofheterologous proteins include enzymes such as hydrolases includingproteases, cellulases, amylases, carbohydrases, and lipases; isomerasessuch as racemases, epimerases, tautomerases, or mutases; transferases,kinases and phophatases. In some embodiments, the proteins aretherapeutically significant proteins or peptides, including but notlimited to growth factors, cytokines, ligands, receptors and inhibitors,as well as vaccines and antibodies. In additional embodiments, theproteins are commercially important industrial proteins/peptides (e.g.,proteases, carbohydrases such as amylases and glucoamylases, cellulases,oxidases and lipases). In some embodiments, the gene encoding theproteins are naturally occurring genes, while in other embodiments,mutated and/or synthetic genes are used.

As used herein, “homologous protein” refers to a protein or polypeptidenative or naturally occurring in a cell. In preferred embodiments, thecell is a Gram-positive cell, while in particularly preferredembodiments, the cell is a Bacillus host cell. In alternativeembodiments, the homologous protein is a native protein produced byother organisms, including but not limited to E. coli. The inventionencompasses host cells producing the homologous protein via recombinantDNA technology.

As used herein, an “operon region” comprises a group of contiguous genesthat are transcribed as a single transcription unit from a commonpromoter, and are thereby subject to co-regulation. In some embodiments,the operon includes a regulator gene. In most preferred embodiments,operons that are highly expressed as measured by RNA levels, but have anunknown or unnecessary function are used.

As used herein, a “multi-contiguous single gene region” is a regionwherein at least the coding regions of two genes occur in tandem and insome embodiments, include intervening sequences preceding and followingthe coding regions. In some embodiments, an antimicrobial region isincluded.

As used herein, an “antimicrobial region” is a region containing atleast one gene that encodes an antimicrobial protein.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides cells that have been geneticallymanipulated to have an altered capacity to produce expressed proteins.In particular, the present invention relates to Gram-positivemicroorganisms, such as Bacillus species having enhanced expression of aprotein of interest, wherein one or more chromosomal genes have beeninactivated, and preferably wherein one or more chromosomal genes havebeen deleted from the Bacillus chromosome. In some further embodiments,one or more indigenous chromosomal regions have been deleted from acorresponding wild-type Bacillus host chromosome. Indeed, the presentinvention provides means for deletion of single or multiple genes, aswell as large chromosomal deletions. In preferred embodiments, suchdeletions provide advantages such as improved production of a protein ofinterest.

A. Gene Deletions

As indicated above, the present invention includes embodiments thatinvolve singe or multiple gene deletions and/or mutations, as well aslarge chromosomal deletions.

In some preferred embodiments, the present invention includes a DNAconstruct comprising an incoming sequence. The DNA construct isassembled in vitro, followed by direct cloning of the construct into acompetent Bacillus host, such that the DNA construct becomes integratedinto the Bacillus chromosome. For example, PCR fusion and/or ligationcan be employed to assemble a DNA construct in vitro. In someembodiments, the DNA construct is a non-plasmid construct, while inother embodiments it is incorporated into a vector (e.g., a plasmid). Insome embodiments, circular plasmids are used. In preferred embodiments,circular plasmids are designed to use an appropriate restriction enzyme(i.e., one that does not disrupt the DNA construct). Thus, linearplasmids find use in the present invention (See, FIG. 1). However, othermethods are suitable for use in the present invention, as known to thosein the art (See e.g., Perego, “Integrational Vectors for GeneticManipulation in Bacillus subtilis,” in (Sonenshein et al., (eds.).Bacillus subtilis and Other Gram-Positive Bacteria, American Society forMicrobiology, Washington, D.C. [1993]).

In some embodiments, the incoming sequence includes a selective marker.In some preferred embodiments, the incoming sequence includes achromosomal gene selected from the group consisting of sbo, slr, ybcO,csn, spoIISA, phrC, sigB, rapA, CssS, trpA, trpB, trpC, trpD, trpE,trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM,rocF, and rocD or fragments of any of these genes (alone or incombination). In additional embodiments, the incoming sequence includesa homologous sbo, slr, ybcO, csn, spoIISA, phrC, sigB, rapA, CssS trpA,trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA,fbp, rocA, ycgN, ycgM, rocF, and/or rocD gene sequence. A homologoussequence is a nucleic acid sequence having at least 99%, 98%, 97%, 96%,95%, 94% 93%, 92%, 91%, 90%, 88%, 85% or 80% sequence identity to a sbo,slr, ybcO, csn, spoIISA, phrC, sigB, rapA, CssS trpA, trpB, trpC, trpD,trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN,ycgM, rocF, and rocD gene or gene fragment thereof, which may beincluded in the incoming sequence. In preferred embodiments, theincoming sequence comprising a homologous sequence comprises at least95% sequence identity to a sbo, slr, ybcO, csn, spoIISA, phrC, sigB,rapA, CssS trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD,prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, or rocD gene or genefragment of any of these genes. In yet other embodiments, the incomingsequence comprises a selective marker flanked on the 5′ and 3′ ends witha fragment of the gene sequence. In some embodiments, when the DNAconstruct comprising the selective marker and gene, gene fragment orhomologous sequence thereto is transformed into a host cell, thelocation of the selective marker renders the gene non-functional for itsintended purpose. In some embodiments, the incoming sequence comprisesthe selective marker located in the promoter region of the gene. Inother embodiments, the incoming sequence comprises the selective markerlocated after the promoter region of gene. In yet other embodiments, theincoming sequence comprises the selective marker located in the codingregion of the gene. In further embodiments, the incoming sequencecomprises a selective marker flanked by a homology box on both ends. Instill further embodiments, the incoming sequence includes a sequencethat interrupts the transcription and/or translation of the codingsequence. In yet additional embodiments, the DNA construct includesrestriction sites engineered at the upstream and downstream ends of theconstruct.

Whether the DNA construct is incorporated into a vector or used withoutthe presence of plasmid DNA, it is used to transform microorganisms. Itis contemplated that any suitable method for transformation will finduse with the present invention. In preferred embodiments, at least onecopy of the DNA construct is integrated into the host Bacilluschromosome. In some embodiments, one or more DNA constructs of theinvention are used to transform host cells. For example, one DNAconstruct may be used to inactivate a slr gene and another construct maybe used to inactivate a phrC gene. Of course, additional combinationsare contemplated and provided by the present invention.

In some preferred embodiments, the DNA construct also includes apolynucleotide encoding a protein of interest. In some of thesepreferred embodiments, the DNA construct also includes a constitutive orinducible promoter that is operably linked to the sequence encoding theprotein of interest. In some preferred embodiments in which the proteinof interest is a protease, the promoter is selected from the groupconsisting of a tac promoter, a β-lactamase promoter, or an aprEpromoter (DeBoer et al., Proc. Natl. Acad. Sci. USA 80:21-25 [1983]).However, it is not intended that the present invention be limited to anyparticular promoter, as any suitable promoter known to those in the artfinds use with the present invention. Nonetheless, in particularlypreferred embodiments, the promoter is the B. subtilis aprE promoter.

Various methods are known for the transformation of Bacillus species.Indeed, methods for altering the chromosome of Bacillus involvingplasmid constructs and transformation of the plasmids into E. coli arewell known. In most methods, plasmids are subsequently isolated from E.coli and transformed into Bacillus. However, it is not essential to usesuch intervening microorganisms such as E. coli, and in some preferredembodiments, the DNA construct is directly transformed into a competentBacillus host.

In some embodiments, the well-known Bacillus subtilis strain 168 findsuse in the present invention. Indeed, the genome of this strain has beenwell-characterized (See, Kunst et al., Nature 390:249-256 [1997]; andHenner et al., Microbiol. Rev., 44:57-82 [1980]). The genome iscomprised of one 4215 kb chromosome. While the coordinates used hereinrefer to the 168 strain, the invention encompasses analogous sequencesfrom Bacillus strains.

In some embodiments, the incoming chromosomal sequence includes one ormore genes selected from the group consisting of sbo, slr, ybcO, csn,spoIISA, sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF,tdh/kbl, alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, androcD gene fragments thereof and homologous sequences thereto. The DNAcoding sequences of these genes from B. subtilis 168 are provided in SEQID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ IDNO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:39, SEQ IDNO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ IDNO:50, SEQ ID NO:37, SEQ ID NO:25, SEQ ID NO:21, SEQ ID NO:50, SEQ IDNO:29, SEQ ID NO:23, SEQ ID NO:27, SEQ ID NO:19, SEQ ID NO:31, SEQ IDNO:48, SEQ ID NO:46, SEQ ID NO:35, and SEQ ID NO:33.

As mentioned above, in some embodiments, the incoming sequence whichcomprises a sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS, trpA,trpB, trpC, trpD, trpE, trpF, tdh, kbl, alsD, sigD, prpC, gapB, pckA,fbp, rocA, ycgN, ycgM, rocF, and rocD gene, a gene fragment thereof, ora homologous sequence thereto includes the coding region and may furtherinclude immediate chromosomal coding region flanking sequences. In someembodiments the coding region flanking sequences include a range ofabout 1 bp to 2500 bp; about 1 bp to 1500 bp, about 1 bp to 1000 bp,about 1 bp to 500 bp, and 1 bp to 250 bp. The number of nucleic acidsequences comprising the coding region flanking sequence may bedifferent on each end of the gene coding sequence. For example, in someembodiments, the 5′ end of the coding sequence includes less than 25 bpand the 3′ end of the coding sequence includes more than 100 bp.Sequences of these genes and gene products are provided below. Thenumbering used herein is that used in subtilist (See e.g., Moszer etal., Microbiol., 141:261-268 [1995]).

The sbo coding sequence of B. subtilis 168 is shown below: (SEQ ID NO:1)ATGAAAAAAGCTGTCATTGTAGAAAACAAAGGTTGTGCAACATGCTCGATCGGAGCCGCTTGTCTAGTGGACGGTCCTATCCCTGATTTTGAAATTGCCGGTGCAACAGGTCTATTCGGTCTATGGGGG.

The deduced amino acid sequence for Sbo is: (SEQ ID NO:2)MKKAVIVENKGCATCSIGAACLVDGPIPDFEIAGATGLFGLWG.

In one embodiment, the gene region found at about 3834868 to 3835219 bpof the B. subtilis 168 chromosome was deleted using the presentinvention. The sbo coding region found at about 3835081 to 3835209produces subtilisin A, an antimicrobial that has activity against someGram-positive bacteria. (See, Zheng et al., J. Bacteriol., 181:7346-7355[1994]).

The slr coding sequence of B. subtilis 168 is shown below: (SEQ ID NO:3)ATGATTGGAAGAATTATCCGTTTGTACCGTAAAAGAAAAGGCTATTCTATTAATCAGCTGGCTGTTGAGTCAGGCGTATCCAAATCCTATTTAAGCAAGATTGAAAGAGGCGTTCACACGAATCCGTCCGTTCAATTTTTAAAAAAAGTTTCTGCCACACTGGAAGTTGAATTAACAGAATTATTTGACGCAGAAACAATGATGTATGAAAAAATCAGCGGCGGTGAAGAAGAATGGCGCGTACATTTAGTGCAAGCCGTACAAGCCGGGATGGAAAAGGAAGAATTGTTCACTTTTACGAACAGACTCAAGAAAGAACAGCCTGAAACTGCCTCTTACCGCAACCGCAAACTGACGGAATCCAATATAGAAGAATGGAAAGCGCTGATGGCGGAGGCAAGAGAAATCGGCTTGTCTGTCCATGAAGTCAAATCCTTTTTAAAAACAAAG GGAAGA.

The deduced amino acid sequence for Slr is: (SEQ ID NO:4)MIGRIIRLYRKRKGYSINQLAVESGVSKSYLSKIERGVHTNPSVQFLKKVSATLEVELTELFDAETMMYEKISGGEEEWRVHLVQAVQAGMEKEELFTFTNRLKKEQPETASYRNRKLTESNIEEWKALMAEAREIGLSVHEVKSFLKTK GR.

In one embodiment, the sequence found at about 3529014-3529603 bp of theB. subtilis 168 chromosome was deleted using the present invention. Theslr coding sequence is found at about 3529131 to 3529586 of thechromosome.

The phrC coding sequence of B. subtilis 168 is provided below: (SEQ IDNO:13) ATGAAATTGAAATCTAAGTTGTTTGTTATTTGTTTGGCCGCAGCCGCGATTTTTACAGCGGCTGGCGTTTCTGCTAATGCGGAAGCACTCGACTTTCATG TGACAGAAAGAGGAATGACG.

The deduced amino acid sequence for PhrC is: (SEQ ID NO:14)MKLKSKLFVICLAAAAIFTAAGVSANAEALDFHVTERGMT

Additionally, the coding region found at about 429531 to 429650 bp ofthe B. subtilis 168 chromosome was inactivated by an insertion of aselective marker at 429591 of the coding sequence.

The sigB coding sequence of B. subtilis 168 is shown below: (SEQ IDNO:9) TTGATCATGACACAACCATCAAAAACTACGAAACTAACTAAAGATGAAGTCGATCGGCTCATAAGCGATTACCAAACAAAGCAAGATGAACAAGCGCAGGAAACGCTTGTGCGGGTGTATACAAATCTGGTTGACATGCTTGCGAAAAAATACTCAAAAGGCAAAAGCTTCCACGAGGATCTCCGCCAGGTCGGCATGATCGGGCTGCTAGGCGCGATTAAGCGATACGATCCTGTTGTCGGCAAATCGTTTGAAGCTTTTGCAATCCCGACAATCATCGGTGAAATTAAACGTTTCCTCAGAGATAAAACATGGAGCGTTCATGTGCCGAGACGAATTAAAGAACTCGGTCCAAGAATCAAAATGGCGGTTGATCAGCTGACCACTGAAACACAAAGATCGCCGAAAGTCGAAGAGATTGCCGAATTCCTCGATGTTTCTGAAGAAGAGGTTCTTGAAACGATGGAAATGGGCAAAAGCTATCAAGCCTTATCCGTTGACCACAGCATTGAAGCGGATTCGGACGGAAGCACTGTCACGATTCTTGATATCGTCGGATCACAGGAGGACGGATATGAGCGGGTCAACCAGCAATTGATGCTGCAAAGCGTGCTTCATGTCCTUCAGACCGTGAGAAACAAATCATAGACCTTACGTATATTCAAAACAAAAGCCAAAAAGAAACTGGGGACATTCTCGGTATATCTCAAATGCACGTCTCGCGCTTGCAACGCAAAGCTGTGAAGAAGCTCAGAGAGGCCTTGATTGAAGATCCCTCGATGGAGTTAATG.

The deduced amino acid sequence for SigB is: (SEQ ID NO:10)MIMTQPSKTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADSDGSTVTILDIVGSQEDGYERVNQQLMLQSVLHVLSDREKQIIDLTYIQNKSQKETGDILGISQMHVSRLQRKAVKK LREALIEDPSMELM.

Additionally, the coding sequence is found at about 522417 to 5232085 bpof the B. subtilis 168 chromosome.

The spoIISA coding sequence of B. subtilis 168 is shown below: (SEQ IDNO:11) ATGGTTTTATTCTTTCAGATCATGGTCTGGTGCATCGTGGCCGGACTGGGGTTATACGTGTATGCCACGTGGCGTTTCGAAGCGAAGGTCAAAGAAAAAATGTCCGCCATTCGGAAAACTTGGTATTTGCTGTTTGTTCTGGGCGCTATGGTATACTGGACATATGAGCCCACTTCCCTATTTACCCACTGGGAACGGTATCTCATTGTCGCAGTCAGTTTTGCTTTGATTGATGCTTTTATCTTCTTAAGTGCATATGTCAAAAAACTGGCCGGCAGCGAGCTTGAAACAGACACAAGAGAAATTCTTGAAGAAAACAACGAAATGCTCCACATGTATCTCAATCGGCTGAAAACATACCAATACCTATTGAAAAACGAACCGATCCATGTTTATTATGGAAGTATAGATGCTTATGCTGAAGGTATTGATAAGCTGCTGAAAACCTATGCTGATAAAATGAACTTAACGGCTTCTCTTTGCCACTATTCGACACAGGCTGATAAAGACCGGTTAACCGAGCATATGGATGATCCGGCAGATGTACAAACACGGCTCGATCGAAAGGATGTTTATTACGACCAATACGGAAAAGTGGTTCTCATCCCTTTTACCATCGAGACACAGAACTATGTCATCAAGCTGACGTCTGACAGCATTGTCACGGAATTTGATTATTTGCTATTTACGTCATTAACGAGCATATATGATTTGGTGCTGCCAATTGAGGAGGAAGGTGAAGGA.

The deduced amino acid sequence for SpoIISA is: (SEQ ID NO: 12)MVLFFQIMVWCIVAGLGLYVYATWRFEAKVKEKMSAIRKTWYLLFVLGAMVYWTYEPTSLFTHWERYLIVAVSFALIDAFIFLSAYVKKLAGSELETDTREILEENNEMLHMYLNRLKTYQYLLKNEPIHVYYGSIDAYAEGIDKLLKTYADKMNLTASLCHYSTQADKDRLTEHMDDPADVQTRLDRKDVYYDQYGKVVLIPFTIETQNYVIKLTSDSIVTEFDYLLFTSLTSIYDLVLPIEEEGEG.

Additionally, the coding region is found at about 1347587 to 1348714 bpof the B. subtilis 168 chromosome.

The csn coding sequence of B. subtilis 168 is shown below: (SEQ ID NO:7)ATGAAAATCAGTATGCAAAAAGCAGATTTTTGGAAAAAAGCAGCGATCTCATTACTTGTTTTCACCATGTTTTTTACCCTGATGATGAGCGAAACGGTTTTTGCGGCGGGACTGAATAAAGATCAAAAGCGCCGGGCGGAACAGCTGACAAGTATCTTTGAAAACGGCACAACGGAGATCCAATATGGATATGTAGAGCGATTGGATGACGGGCGAGGCTATACATGCGGACGGGCAGGCTTTACAACGGCTACCGGGGATGCATTGGAAGTAGTGGAAGTATACACAAAGGCAGTTCCGAATAACAAACTGAAAAAGTATCTGCCTGAATTGCGCCGTCTGGCCAAGGAAGAAAGCGATGATACAAGCAATCTCAAGGGATTCGCTTCTGCCTGGAAGTCGCTTGCAAATGATAAGGAATTTCGCGCCGCTCAAGACAAAGTAAATGACCATTTGTATTATCAGCCTGCCATGAAACGATCGGATAATGCCGGACTAAAAACAGCATTGGCAAGAGCTGTGATGTACGATACGGTTATTCAGCATGGCGATGGTGATGACCCTGACTCTTTTTATGCCTTGATTAAACGTACGAACAAAAAAGCGGGCGGATCACCTAAAGACGGAATAGACGAGAAGAAGTGGTTGAATAAATTCTTGGACGTACGCTATGACGATCTGATGAATCCGGCCAATCATGACACCCGTGACGAATGGAGAGAATCAGTTGCCCGTGTGGACGTGCTTCGCTCTATCGCCAAGGAGAACAACTATAATCTAAACGGACCGATTCATGTTCGTTCAAACGAGTACGGTAATTTTGTAATCAAA.

The deduced amino acid sequence for Csn is: (SEQ ID NO: 8)MKISMQKADFWKKAAISLLVFTMFFTLMMSETVFAAGLNKDQKRRAEQLTSIFENGTTETQYGYVERLDDGRGYTCGRAGFTTATGDALEVVEVYTKAVPNNKLKKYLPELRRLAKEESDDTSNLKGFASAWKSLANDKEFRAAQDKVNDHLYYQPAMKRSDNAGLKTALARAVMYDTVIQHGDGDDPDSFYALIKRTNKKAGGSPKDGIDEKKWLNKFLDVRYDDLMNPANHDTRDEWRESVARVDVLRSIAKENNYNLNGPIHVRSNEYGNFVIK.

Additionally, the coding region is found at about 2747213 to 2748043 bpof the B. subtilis 168 chromosome.

The ybcO coding sequence of B. subtilis 168 is shown below: (SEQ IDNO:5) ATGAAAAGAAACCAAAAAGAATGGGAATCTGTGAGTAAAAAAGGACTTATGAAGCCGGGAGGTACTTCGATTGTGAAAGCTGCTGGCTGCATGGGCTGTTGGGCCTCGAAGAGTATTGCTATGACACGTGTTTGTGCACTTCCGCATCCT GCTATGAGAGCTATT.

The deduced amino acid sequence for YbcO is: (SEQ ID NO: 6)MKRNQKEWESVSKKGLMKPGGTSIVKAAGCMGCWASKSIAMTRVCALPHP AMRAI.

Additionally, the coding region is found at about 213926 to 214090 bp ofthe B. subtilis 168 chromosome.

The rapA coding sequence of B. subtilis 168 is shown below: (SEQ IDNO:15) TTGAGGATGAAGCAGACGATTCCGTCCTCTTATGTCGGGCTTAAAAATTAATGAATGGTATACTCATATCCGGCAGTTCCACGTCGCTGAAGCCGAACGGTCAAGCTCGAAGTAGAAAGAGAAATTGAGGATATGGAAGAAGACCAAGATTTGCTGCTGTATTATTCTTTAATGGAGTTCAGGCACCGTGTCATGCTGGATTACATTAAGCCTTTTGGAGAGGACACGTCGCAGCTAGAGTTTTCAGAATTGTTAGAAGACATCGAAGGGAATCAGTACAAGCTGACAGGGCTTCTCGAATATTACTTTAATTTTTTTCGAGGAATGTATGAATTTAAGCAGAAGATGTTTGTCAGTGCCATGATGTATTATAAACGGGCAGAAAAGAATCTTGCCCTCGTCTCGGATGATATTGAGAAAGCAGAGTTTGCTTTTAAAATGGCTGAGATTTTTTACAATTTAAAACAAACCTATGTTTCGATGAGCTACGCCGTTCAGGCATTAGAAACATACCAAATGTATGAAACGTACACCGTCCGCAGAATCCAATGTGAATTCGTTATTGCAGGTAATTATGATGATATGCAGTATCCAGAAAGAGCATTGCCCCACTTAGAACTGGCTTTAGATCTTGCAAAGAAAGAAGGCAATCCCCGCCTGATCAGTTCTGCCCTATATAATCTCGGAAACTGCTATGAGAAAATGGGTGAACTGCAAAAGGCAGCCGAATACTTTGGGAAATCTGTTTCTATTTGCAAGTCGGAAAAGTTCGATAATCTTCCGCATTCTATCTACTCTTTAACACAAGTTCTGTATAAACAAAAAAATGACGCCGAAGCGCAAAAAAAGTATCGTGAAGGATTGGAAATCGCCCGTCAATACAGTGATGAATTATTTGTGGAGCTTTTTCAATTTTTACATGCGTTATACGGTTATCGGAAAAAACAATTGACACAGAATCAGTCTCACACACCTTTCAATTTCTTGAAGAACATATGCTGTATCCTTATATTGAAGAGCTGGCGCATGATGCTGCCCAATTCTATATAGAAAACGGACAGCCCGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATC.

The deduced amino acid sequence for RapA is: (SEQ ID NO: 16)MRMKQTIPSSYVGLKINEWYTHIRQFHVAEAERVKLEVEREIEDMEEDQDLLLYYSLMEFRHRVMLDYIKPFGEDTSQLEFSELLEDIEGNQYKLTGLLEYYFNFFRGMYEFKQKMFVSAMMYYKRAEKNLALVSDDIEKAEFAFKMAEIFYNLKQTYVSMSYAVQALETYQMYETYTVRRIQCEFVIAGNYDDMQYPERALPHLELALDLAKKEGNPRLISSALYNLGNCYEKMGELQKAAEYFGKSVSICKSEKFDNLPHSIYSLTQVLYKQKNDAEAQKKYREGLEIARQYSDELFVELFQFLHALYGKNIDTESVSHTFQFLEEHMLYPYIEELAHDAAQFYIENGQPEKALSFYEKMVHAQKQIQRGDCLYEI

Additionally, the coding region is found at about 1315179 to 1316312 bpof the B. subtilis 168 chromosome.

The Css coding sequence of B. subtilis 168 is shown below: (SEQ IDNO:17) ATGAAAAACAAGCCGCTCGCGTTTCAGATATGGGTTGTCATATCCGGCATCCTGTTAGCGATATCGATTTTACTGCTTGTGTTATTTTCAAACACGCTGCGAGATTTTTTCACTAATGAAACGTATACGACGATTGAAAATGAGCAGCATGTTCTGACAGAGTACCGCCTGCCAGGTTCGATTGAAAGGCGCTATTACAGCGAGGAAGCGACGGCGCCGACAACTGTCCGCTCCGTACAGCACGTGCTCCTTCCTGAAAATGAAGAGGCTTCTTCAGACAAGGATTTAAGCATTCTGTCATCTTCATTTATCCACAAGGTGTACAAGCTGGCTGATAAGCAGGAAGCTAAAAAGAAACGTTACAGCGCCGACGTCAATGGAGAGAAAGTGTTTTTTGTCATTAAAAAGGGACTTTCCGTCAATGGACAATCAGCGATGATGCTCTCTTACGCGCTTGATTCTTATCGGGACGATTTGGCCTATACCTTGTTCAAACAGCTTCTGTTTATTATAGCTGTCGTCATTTTATTAAGCTGGATTCCGGCTATTTGGCTTGCAAAGTATTTATCAAGGCCTCTTGTATCATTTGAAAAACACGTCAAACGGATTTCTGAACAGGATTGGGATGACCCAGTAAAAGTGGACCGGAAAGATGAAATCGGCAAATTGGGCCATACCATCGAAGAGATGCGCCAAAAGCTTGTGCAAAAGGATGAAACAGAAAGAACTCTATTGCAAAATATCTCTCATGATTTAAAAACGCCGGTCATGGTCATCAGAGGCTATACACAATCAATTAAAGACGGGATTTTTCCTAAAGGAGACCTTGAAAACACTGTAGATGTTATTGAATGCGAAGCTCTTAAGCTGGAGAAAAAAATAAAGGATTTATTATATTTAACGAAGCTGGATTATTTAGCGAAGCAAAAAGTGCAGCACGACATGTTCAGTATTGTGGAAGTGACAGAAGAAGTCATCGAACGATTGAAGTGGGCGCGGAAAGAACTATCGTGGGAAATTGATGTAGAAGAGGATATTTTGATGCCGGGCGATCCGGAGCAATGGAACAAACTCCTCGAAAACATTTTGGAAAATCAAATCCGCTATGCTGAGACAAAAATAGAAATCAGCATGAAACAAGATGATCGAAATATCGTGATCACCATTAAAAATGACGGTCCGCATATTGAAGATGAGATGCTCTCCAGCCTCTATGAGCCTTTTAATAAAGGGAAGAAAGGCGAATTCGGCATTGGTCTAAGCATCGTAAAACGAATTTTAACTCTTCATAAGGCATCTATCTCAATTGAAAATGACAAAACGGGTGTATCATACCGCATAGCAGTGCCA AAA.

The deduced amino acid sequence for Css (GenBank Accession No. 032193)is: (SEQ ID NO:18) MKNKPLAFQIWVVISGILLAISILLLVLFSNTLRDFFTNETYTTIENEQHVLTEYRLPGSIERRYYSEEATAPTTVRSVQHVLLPENEEASSDKDLSILSSSFIHKVYKLADKQEAKKKRYSADVNGEKVFFVIKKGLSVNGQSAMMLSYALDSYRDDLAYTLFKQLLFIIAWILLSWIPAIWLAKYLSRPLVSFEKHVKRISEQDWDDPVKVDRKDEIGKLGHTIEEMRQKLVQKDETERTLLQNISHDLKTPVMVIRGYTQSIKDGIFPKGDLENTVDVIECEALKLEKKIKDLLYLTKLDYLAKQKVQHDMFSIVEVTEEVIERLKWARKELSWEIVEEDILMPGDPEQWNKLLENILENQIRYAETKIEISMKQDDRNIVITIKNDGPHIEDEMLSSLYEPFNKGKKGEFGIGLSIVKRILTLHKASISIENDKTGVSYRIAVPK.

Additionally, the gene region is found at about 3384612 to 3386774 bp ofthe B. subtilis 168 chromosome.

The fbp coding sequence of the Fbp protein (fructose-1,6-biophosphatase)of B. subtilis 168 is shown below: (SEQ ID NO:19)ATGTTTAAAAATAATGTCATACTTTTAAATTCACCTTATCATGCACATGCTCATAAAGAGGGGTTTATTCTAAAAAGGGGATGGACGGTTTTGGAAAGCAAGTACCTAGATCTACTCGCACAAAAATACGATTGTGAAGAAAAAGTGGTAACAGAAATCATCAATTTGAAAGCGATATTGAACCTGCCAAAAGGCACCGAGCATTTTGTCAGTGATCTGCACGGAGAGTATCAGGCATTCCAGCACGTGTTGCGCAATGGTTCAGGACGAGTCAAAGAGAAGATACGCGACATCTTCAGCGGTGTCATTTACGATAGAGAAATTGATGAATTAGCAGCATTGGTCTATTATCCGGAAGACAAACTGAAATTAATCAAACATGACTTTGATGCGAAAGAAGCGTTAAACGAGTGGTATAAAGAAACGATTCATCGAATGATTAAGCTCGTTTCATATTGCTCCTCTAAGTATACCCGCTCCAAATTACGCAAAGCACTGCCTGCCCAATTTGCTTATATTACGGAGGAGCTGTTATACAAAACAGAACAAGCTGGCAACAAGGAGCAATATTACTCCGAAATCATTGATCAGATCATTGAACTTGGCCAAGCCGATAAGCTGATCACCGGCCTTGCTTACAGCGTTCAGCGATTGGTGGTCGACCATCTGCATGTGGTCGGCGATATTTATGACCGCGGCCCGCAGCCGGATAGAATTATGGAAGAACTGATCAACTATCATTCTGTCGATATTCAGTGGGGAAATCACGATGTCCTTTGGATCGGCGCCTATTCCGGTTCCAAAGTGTGCCTGGCCAATATTATCCGCATCTGTGCCCGCTACGACAACCTGGATATTATTGAGGACGTGTACGGCATCAACCTGAGACCGCTGCTGAACCTGGCCGAAAAATATTATGATGATAATCCAGCGTTCCGTCCAAAAGCAGACGAAAACAGGCCAGAGGATGAGATTAAGCAAATCACAAAAATCCATCAAGCGATTGCCATGATCCAATTCAAGCTTGAGAGCCCGATTATCAAGAGACGGCCGAACTTTAATATGGAAGAGCGGCTGTTATTAGAGAAAATAGACTATGACAAAAATGAAATCACGCTGAACGGAAAAACATATCAACTGGAAAACACCTGCTTTGCGACGATTAATCCGGAGCAGCCAGATCAGCTATTAGAAGAAGAAGCAGAAGTCATAGACAAGCTGCTATTCTCTGTCCAGCATTCCGAAAAGCTGGGCCGCCATATGAATTTTATGATGAAAAAAGGCAGCCTTTATTTAAAATATAACGGCAACCTGTTGATTCACGGCTGTATTCCAGTTGATGAAAACGGCAATATGGAAACGATGATGATTGAGGATAAACCGTATGCGGGCCGTGAGCTGCTCGATGTATTTGAACGATTCTTGCGGGAAGCCTTTGCCCACCCGGAAGAAACCGATGACCTGGCGACAGATATGGCTTGGTATTTATGGACAGGCGAATACTCCTCCCTCTTCGGAAAACGCGCCATGACGACATTTGAGCGCTATTTCATCAAAGAGAAGGAAACGCATAAAGAGAAGAAAAACCCGTATTATTATTTACGAGAAGACGAGGCAACCTGCCGAAACATCCTGGCAGAATTCGGCCTCAATCCAGATCACGGCCATATCATCAACGGCCATACACCTGTAAAAGAAATCGAAGGAGAAGACCCAATCAAAGCAAACGGAAAAATGATCGTCATCGACGGCGGCTTCTCCAAAGCCTACCAATCCACAACAGGCATCGCCGGCTACACGCTGCTATACAACTCCTACGGCATGCAGCTCGTCGCCCATAAACACTTCAATTCCAAGGCAGAAGTCCTAAGCACCGGAACCGACGTCTTAACGGTCAAACGATTAGTGGACAAAGAGCTTGAGCGGAAGAAAGTGAAGGAAACGAATGTGGGTGAGGAATTGTTGCAGGAAGTTGCGATTTTAGAGAGTTTGCGGGAGTA TCGGTATATGAAG.

The deduced amino acid sequence of the Fbp protein is: (SEQ ID NO:20)MFKNNVILLNSPYHAHAHKEGFILKRGWTVLESKYLDLLAQKYDCEEKVVTEIINLKAILNLPKGTEHFVSDLHGEYQAFQHVLRNGSGRVKEKIRDIFSGVIYDREIDELAALVYYPEDKLKLIKHDFDAKEALNEWYKETIHRMIKLVSYCSSKYTRSKLRKALPAQFAYITEELLYKTEQAGNKEQYYSEIIDQIIELGQADKLITGLAYSVQRLWDHLHVVGDIYDRGPQPDRIMEELINYHSVDIQWGNHDVLWIGAYSGSKVCLANIIRICARYDNLDIIEDVYGINLRPLLNLAEKYYDDNPAFRPKADENRPEDEIKQITKIHQAIAMIQFKLESPIIKRRPNFNMEERLLLEKIDYDKNEITLNGKTYQLENTCFATINPEQPDQLLEEEAEVIDKLLFSVQHSEKLGRHMNFMMKKGSLYLKYNGNLLIHGCIPVDENGNMETMMIEDKPYAGRELLDVFERFLREAFAHPEETDDLATDMAWYLWTGEYSSLFGKRAMTTFERYFIKEKETHKEKKNPYYYLREDEATCRNILAEFGLNPDHGHIINGHTPVKEIEGEDPIKANGKMIVIDGGFSKAYQSTTGIAGYTLLYNSYGMQLVAHKHFNSKAEVLSTGTDVLTVKRLVDKELERKKVKETNVG EELLQEVAILESLREYRYMK.

Additionally, the coding region is found at about 4127053 to 4129065 bpof the B. subtilis 168 chromosome.

The alsD coding sequence of the alsD protein (alpha-acetolactatedecarboxylase) of B. subtilis 168 is shown below: (SEQ ID NO:21)ATGAAACGAGAAAGCAACATTCAAGTGCTCAGCCGTGGTCAAAAAGATCAGCCTGTGAGCCAGATTTATCAAGTATCAACAATGACTTCTCTATTAGACGGAGTATATGACGGAGATTTTGAACTGTCAGAGATTCCGAAATATGGAGACTTCGGTATCGGAACCTTTAACAAGCTTGACGGAGAGCTGATTGGGTTTGACGGCGAATTTTACCGTCTTCGCTCAGACGGAACCGCGACACCGGTCCAAAATGGAGACCGTTCACCGTTCTGTTCATTTACGTTCTTTACACCGGACATGACGCACAAAATTGATGCGAAAATGACACGCGAAGACTTTGAAAAAGAGATCAACAGCATGCTGCCAAGCAGAAACTTATTTTATGCAATTCGCATTGACGGATTGTTTAAAAAGGTGCAGACAAGAACAGTAGAACTTCAAGAAAAACCTTACGTGCCAATGGTTGAAGCGGTCAAAACACAGCCGATTTTCAACTTCGACAACGTGAGAGGAACGATTGTAGGTTTCTTGACACCAGCTTATGCAAACGGAATCGCCGTTTCTGGCTATCACCTGCACTTCATTGACGAAGGACGCAATTCAGGCGGACACGTTTTTGACTATGTGCTTGAGGATTGCACGGTTACGATTTCTCAAAAAATGAACATGAATCTCAGACTTCCGAACACAGCGGATTTCTTTAATGCGAATCTGGATAACCCTGATTTTGCGAAAGATATCGAAACAACT GAAGGAAGCCCTGAA.

The deduced amino acid sequence AlsD protein sequence is: (SEQ ID NO:22)MKRESNIQVLSRGQKDQPVSQIYQVSTMTSLLDGVYDGDFELSEIPKYGDFGIGTFNKLDGELIGFDGEFYRLRSDGTATPVQNGDRSPFCSFTFFTPDMTHKIDAKMTREDFEKEINSMLPSRNLFYAIRIDGLFKKVQTRTVELQEKPYVPMVEAVKTQPIFNFDNVRGTIVGFLTPAYANGIAVSGYHLHFIDEGRNSGGHVFDYVLEDCTVTISQKMNMNLRLPNTADFFNANLDNPDFAKDIETT EGSPE.

Additionally, the coding region is found at about 3707829-3708593 bp ofthe B. subtilis 168 chromosome.

The gapB coding sequence of the gapB protein (glyceraldehyde-3-phosphatedehydrogenase) of B. subtilis 168 is shown below: (SEQ ID NO:23)ATGAAGGTAAAAGTAGCGATCAACGGGTTTGGAAGAATCGGAAGAATGGTTTTTAGAAAAGCGATGTTAGACGATCAAATTCAAGTAGTGGCCATTAACGCCAGCTATTCCGCAGAAACGCTGGCTCATTTAATAAAGTATGACACAATTCACGGCAGATACGACAAGAGGTTGTGGCTGGTGAAGATAGCCTGATCGTAAATGGAAAGAAAGTGCTTTTGTTAAACAGCCGTGATCCAAAACAGCTGCCTTGGCGGGAATATGATATTGACATAGTCGTCGAAGCAACAGGGAAGTTTAATGCTAAAGATAAAGCGATGGGCCATATAGMGCAGGTGCAAAAAAAGTGATTTTGACCGCTCCGGGAAAAAATGAAGACGTTACCATTGTGATGGGCGTAAATGAGGACCAATTCGACGCTGAGCGCCATGTCATTATTTCAAATGCGTCATGCACGACAAATTGCCTTGCGCCTGTTGTAAAAGTGCTGGATGAAGAGTTTGGCATTGAGAGCGGTCTGATGACTACAGTTCATGCGTATACGAATGACCAAAAAAATATTGATAACCCGCACAAAGATTTGCGCCGGGCGCGGGCTTGCGGTGAATCCATCATTCCAACAACAACAGGAGCGGCAAAGGCGCTTTCGCTTGTGCTGCCGCATCTGAAAGGAAAACTTCACGGCCTCGCCTTGCGTGTCCCTGTTCCGAACGTCTCATTGGTTGATCTCGTTGTTGATCTGAAAACGGATGTTACGGCTGAAGAAGTAAACGAGGCATTTAAACGCGCTGCCAAAACGTCGATGTACGGTGTACTTGATTACTCAGATGAACCGCTCGTTTCGACTGATTATAATACGAATCCGCATTCAGCGGTCATTGACGGGCTTACAACAATGGTAATGGAAGACAGGAAAGTAAAGGTGCTGGCGTGGTATGACAACGAATGGGGCTACTCCTGCAGAGTTGTTGATCTAATCCGCCATGTAGCGGCACGAATG AAACATCCGTCTGCTGTA.

The deduced amino acid sequence of the GapB protein is: (SEQ ID NO:24)MKVKVAINGFGRIGRMVFRKAMLDDQIQVVAINASYSAETLAHLIKYDTIHGRYDKEVVAGEDSLIVNGKKVLLLNSRDPKQLPWREYDIDIWEATGKFNAKDKAMGHIEAGAKKVILTAPGKNEDVTIVMGVNEDQFDAERHVIISNASCTTNCLAPVVKVLDEEFGIESGLMTTVHAYTNDQKNIDNPHKDLRRARACGESIIPTTTGAAKALSLVLPHLKGKLHGLALRVPVPNVSLVDLVVDLKTDVTAEEVNEAFKRAAKTSMYGVLDYSDEPLVSTDYNTNPHSAVIDGLTTMVMEDRKVKVLAWYDNEWGYSCRVVDLIRHVAARMKHPSAV.

Additionally, the coding region is found at about 2966075-2967094 bp ofthe B. subtilis 168 chromosome.

The Kbl coding sequence of the Kbl protein (2-amino-3-ketobutyrate CoAligase) is shown below: (SEQ ID NO:25)ATGACGAAGGAATTTGAGTTTTTAAAAGCAGAGCTTAATAGTATGAAAGAAAACCATACATGGCAAGACATAAAACAGCTTGAATCTATGCAGGGCCCATCTGTCACAGTGAATCACCAAAAAGTCATTCAGCTATCTTCTAATAATTACCTCGGATTCACTTCACATCCTAGACTCATCAACGCCGCACAGGAGGCCGTTCAGCAGTATGGAGCCGGCACCGGATCAGTGAGAACGATTGCGGGTACATTTACAATGCATCAAGAGCTTGAGAAAAAGCTGGCAGCCTTTAAAAAAACGGAGGCGGCACTTGTATTCCAATCAGGCTTCACAACAAACCAAGGCGTACTTTCAAGTATTCTATCAAAAGAGGACATTGTCATCTCAGATGAATTGAACCATGCCTCTATTATTGACGGAATTCGACTGACAAAGGCGGATAAAAAGGTGTATCAGCACGTCAATATGAGTGATTTAGAGCGGGTGCTGAGAAAGTCAATGAATTATCGGATGCGTCTGATTGTGACAGACGGCGTATTTTCCATGGATGGCAACATAGCTCCTCTGCCTGATATTGTAGAGCTCGCTGAGAAATATGACGCATTTGTGATGGTGGATGACGCCCATGCATCCGGAGTACTTGGCGAAAACGGCAGGGGAACGGTGAATCACTTCGGTCTTGACGGCAGAGTGCATATTCAGGTCGGAACATTAAGCAAGGCAATCGGAGTGCTCGGCGGCTACGCTGCAGGTTCAAAGGTGCTGATCGATTATTTGCGCCATAAAGGCCGTCCATTTTTATTCAGCACATCTCATCCGCCGGCAGTCACTGCAGCTTGTATGGAAGCGATTGATGTCTTGCTTGAAGAGCCGGAGCATATGGAGCGCTTGTGGGAGAATACTGCCTATTTTAAAGCAATGCTTGTGAAAATGGGTCTGACTCTCACGAAGAGTGAAACGCCGATTCTTCCTATTTTAATAGGTGATGAAGGTGTGGCAAAGCAATTTTCAGATCAGCTCCTTTCTCGCGGTGTTTTTGCCCAAAGTATCGTTTTCCCGACTGTAGCAAAGGGAAAAGCCAGAATTCGCACGATTATAACAGCAGAGCACACCAAAGATGAACTGGATCAGGCGCTTGATGTCATCGAAAAGACGGCAAAGGAGCTCCAGCTATTG.

The deduced amino acid sequence of the Kbl protein is: (SEQ ID NO:26)MTKEFEFLKAELNSMKENHTWQDIKQLESMQGPSVWNHQKVIQLSSNNYLGFTSHPRLINMQEAVQQYGAGTGSVRTIAGTFTMHQELEKKLMFKKTEMLVFQSGFTTNQGVLSSILSKEDIVISDELNHASIIDGIRLTKADKKVYQHVNMSDLERVLRKSMNYRMRLIVTDGVFSMDGNIAPLPDIVELAEKYDAFVMVDDAHASGVLGENGRGTVNHFGLDGRVHIQVGTLSKAIGVLGGYAAGSKVLIDYLRHKGRPFLFSTSHPPAVTAACMEAIDVLLEEPEHMERLWENTAYFKAMLVKMGLTLTKSETPILPILIGDEGVAKQFSDQLLSRGVFAQSIVFPTVAKGKARIRTIITAEHTKDELDQALDVIEKTAKELQLL.

Additionally, the coding region is found at about 1770787-1771962 bp ofthe B. subtilis 168 chromosome.

The PckA coding sequence of the PckA (phosphoenolpyruvate carboxykinase)of B. subtilis 168 is shown below: (SEQ ID NO:27)ATGAACTCAGTTGATTTGACCGCTGATTTACAAGCCTTATTAACATGTCCAAATGTGCGTCATAATTTATCAGCAGCACAGCTAACAGAAGTCCTCTCCCGAAACGAAGGCATTTTAACATCCACAGGTGCTGTTCGCGCGACAACAGGCGCTTACACAGGACGCTCACCTAAAGATAAATTCATCGTGGAGGAAGAAAGCACGAAAAAATAAGATCGATTGGGGCCCGGTGAATCAGCCGATTTCAGAAGAAGCGTTTGAGCGGCTGTACACGAAAGTTGTCAGCTATTTAAAGGAGCGAGATGAACTGTTTGTTTTCGAAGGATTTGCCGGAGCAGACGAGAAATACAGGCTGCCGATCACTGTCGTAAATGAGTTCGCATGGCACAATTTATTTGCGCGGCAGCTGTTTATCCGTCCGGAAGGAAATGATAAGAAAACAGTTGAGCAGCCGTTCACCATTCTTTCTGCTCCGCATTTCAAAGCGGATCCAAAAACAGACGGCACTCATTCCGAAACGTTTATTATTGTCTCTTTCGAAAAGCGGACAATTTTAATCGGCGGAACTGAGTATGCCGGTGAAATGAAGAAGTCCATTTTCTCCATTATGAATTTCCTGCTGCCTGAAAGAGATATTTTATCTATGCACTGCTCCGCCAATGTCGGTGAAAAAGGCGATGTCGCCCTTTTCTTCGGACTGTCAGGAACAGGAAAGACCACCCTGTCGGCAGATGCTGACCGCAAGCTGATCGGTGACGATGAACATGGCTGGTCTGATACAGGCGTCTTTAATATTGAAGGCGGATGCTACGCTAAGTGTATTCATTTAAGCGAGGGGAGCCGCAAATCTTTAACGCGATCCGCTTCGGGTCTGTTCTCGAAAATGTCGTTGTGGATGAAGATACACGCGAAGCCAATTATGATGATTCCTTCTATACTGAAAACACGCGGGCAGCTTACCCGATTCATATGATTAATAACATCGTGACTCCAAGCATGGCCGGCCATCCGTCAGCCATTGTATTTTTGACGGCTGATGCCTTCGGAGTCCTGCCGCCGATCAGCAAACTAACGAAGGAGCAGGTGATGTACCATTTTTTGAGCGGTTACACGAGTAAGCTTGCCGGAACCGAACGTGGTGTCACGTCTCCTGAAACGACGTTTTCTACATGCTTCGGCTCACCGTTCCTGCCGCTTCCTGCTCACGTCTATGCTGAAATGCTCGGCAAAAAGATCGATGAACACGGCGCAGACGTTTTCTTAGTCAATACCGGATGGACCGGGGGCGGCTACGGCACAGGCGAACGAATGAAGCTTTCTTACACTAGAGCAATGGTCAAAGCAGCGATTGAAGGCAAATTAGAGGATGCTGAAATGATAACTGACGATATTTTCGGCCTGCACATTCCGGCCCATGTTCCTGGCGTTCCTGATCATATCCTTCAGCCTGAAAACACGTGGACCAACAAGGAAGAATACAAAGAAAAAGCAGTCTACCTTGCAAATGAATTCAAAGAGAACTTTAAAAAGTTCGCACATACCGATGCCATCGCCCAGGCAGGCGGCCCTCTCGTA.

The deduced amino acid sequence of the PckA protein is: (SEQ ID NO:28)MNSVDLTADLQALLTCPNVRHNLSAAQLTEKVLSRNEGILTSTGAVRATTGAYTGRSPKDKFIVEEESTKNKIDWGPVNQPISEEAFERLYTKVVSYLKERDELFVFEGFAGADEKYRLPITVVNEFAWHNLFARQLFIRPEGNDKKTVEQPFTILSAPHFKADPKTDGTHSETFIIVSFEKRTILIGGTEYAGEMKKSIFSIMNFLLPERDILSMHCSANVGEKGDVALFFGLSGTGKTTLSADADRKLIGDDEHGWSDTGVFNIEGGCYAKCIHLSEEKEPQIFNAIRFGSVLENVVVDEDTREANYDDSFYTENTRAAYPIHMINNIVTPSMAGHPSAIVFLTADAFGVLPPISKLTKEQVMYHFLSGYTSKLAGTERGVTSPETTFSTCFGSPFLPLPAHVYAEMLGKKIDEHGADVFLVNTGWTGGGYGTGERMKLSYTRAMVKAAIEGKLEDAEMITDDIFGLHIPAHVPGVPDHILQPENTWTNKEEYKEKAVYLANEFKENFKKFAHTDAIAQAGGPLV.

Additionally, the coding region is found at about 3128579-3130159 bp ofthe B. subtilis 168 chromosome.

The prpC coding sequence of the prpC protein (protein phosphatase) of B.subtilis 168 is shown below: (SEQ ID NO:29)TTGTTAACAGCCTTAAAAACAGATACAGGAAAAATCCGCCAGCATAATGAAGATGATGCGGGGATATTCAAGGGGAAAGATGAATTTATATTAGCGGTTGTCGCTGATGGCATGGGCGGCCATCTTGCTGGAGATGTTGCGAGCAAGATGGCTGTGAAAGCCATGGGGGAGAAATGGAATGAAGCAGAGACGATTCCAACTGCGCCCTCGGAATGTGAAAAATGGCTCATTGAACAGATTCTATCGGTAAACAGCAAAATATACGATCACGCTCAAGCCCACGAAGAATGCCAAGGCATGGGGACGACGATTGTATGTGCACTTTTTACGGGGAAAACGGTTTCTGTTGCCCATATCGGAGACAGCAGATGCTATTTGCTTCAGGACGATGATTTCGTTCAAGTGACAGAAGACCATTCGCTTGTAAATGAACTGGTTCGCACTGGAGAGATTTCCAGAGAAGACGCTGAACATCATCCGCGAAAAAATGTGTTGACGAAGGCGCTTGGAACAGACCAGTTAGTCAGTATTGACACCCGTTCCTTTGATATAGAACCCGGAGACAAACTGCTTCTATGTTCTGACGGACTGACAAATAAAGTGGAAGGCACTGAGTTAAAAGACATCCTGCAAAGCGATTCAGCTCCTCAGGAAAAAGTAAACCTGCTTGTGGACAAAGCCAATCAGAATGGCGGAGAAGACAACATTACAGCAGTTTTGCTTGAGCTTGCTTTACAAGTTGAAGAGGGT GAAGATCAGTGC.

The deduced amino acid sequence of the prpC protein is: (SEQ ID NO:30)MLTALKTDTGKIRQHNEDDAGIFKGKDEFILAVVADGMGGHLAGDVASKMAVKAMGEKWNEAETIPTAPSECEKWLIEQILSVNSKIYDHAQAHEECQGMGTTIVCALFTGKTVSVAHIGDSRCYLLQDDDFVQVTEDHSLVNELVRTGEISREDAEHHPRKNVLTKALGTDQLVSIDTRSFDIEPGDKLLLCSDGLTNKVEGTELKDILQSDSAPQEKVNLLVDKANQNGGEDNITAVLLELALQVEEG EDQC.

Additionally, the coding region is found at about 1649684-1650445 bp ofthe B. subtilis 168 chromosome.

The rocA coding sequence of the rocA protein (pyrroline-5 carboxylatedehydrogenase) of B. subtilis 168 is shown below: (SEQ ID NO:31)ATGACAGTCACATACGCGCACGAACCATTTACCGATTTTACGGAAGCAAAGAATAAAACTGCATTTGGGGAGTCATTGGCCTTTGTAAACACTCAGCTCGGCAAGCATTATCCGCTTGTCATAAATGGAGAAAAAATTGAAACGGACCGCAAAATCATTTCTATTAACCCGGCAAATAAAGAAGAGATCATTGGGTACGCGTCTACAGCGGATCAAGAGCTTGCTGAAAAAGCGATGCAAGCCGCATTGCAGGCATTTGATTCCTGGAAAAAACAAAGACCGGAGCACCGCGCAAATATTCTCTTTAAGGCAGCGGCTATTTTGCGCAGAAGAAAGCATGAATTTTCAAGCTATCTTGTGAAGGAAGCAGGAAAACCGTGGAAGGAAGCAGATGCGGACACGGCTGAAGCGATAGACTTTTTAGAGTTCTACGCGCGCCAAATGTTAAAGCTCAAGGAAGGGGCTCCGGTGAAGAGCCGTGCTGGCGAGGTCAATCAATATCATTACGAAGCGCTTGGCGTCGGCATCGTCATTTCTCCATTTAACTTCCCGCTCGCGATTATGGCGGGAACAGCGGTGGCAGCGATTGTGACAGGAAATACGATTCTCTTAAAACCGGCTGACGCAGCCCCGGTAGTGGCAGCAAAATTTGTCGAGGTCATGGAGGAAGCGGGTCTGCCAAACGGCGTTCTGAATTACATTCCGGGAGATGGTGCGGAGATCGGTGATTTCTTAGTTGAGCATCCGAAGACACGGTTTGTCTCATTTACAGGAACCCGTGCAGTCGGCTGCCGGATTTATGAGCGAGCTGCCAAAGTGCAGCCGGGCCATGGCTCAAACGGGTAATTGCAGAAATGGGCGGAAAAGACACAGTGCTTGTCGACAAGGACGCTGATCTTGACCAAGCTGCATCCTCTATCGTGTATTCAGCATAAGGATAAACAGGACAGAAGTGAACTGCGGGCTCCCGCGCGGTCATTCATCAGGATGTGTATGATGAAGTGGTGGAAAAAGCTGTGGCGCTGACCAAAACGCTGACTGTCGGCAATCCAGAAGATCCTGATACGTATATGGGTCCCGTGATTCATGAAGCATCCTACAACAAAGTGATGATACATTGAAATCGGCAAATCTGAAGGCAAGCTATTGGCCGGCGGAGAAGGCGATGATTCAAAAGGCTACTTTATTCAGCCGACGATCTTTGCAGATGTTGATGAAAACGCCCGCTTGATGCAGGAAGAATAACGGCCCGGTTGTTGCGATTTGCAAAGCGCGTGATTTCGATCATATGCTGGAGAAAGCCAATAACACGGAATACGGATTAACAGGTGCGCTTCTGACGAACCGTGCGCACAAAGAACGGGCGCGCGAGGATTTCCATGTCGGAAACCTATATTTTAACAGAGGATGTACCGGAGCAATTGTCGGCTATCAGCCGTTCGGCGGTTTTAATATGTCAGGAACAGACTCAAAAGCAGGCGGTCCCGATTACTTAATTCTTCATATGCAAGCCCAACGTCCGAAGCTTTT.

The deduced amino acid sequence of the RocA protein is: (SEQ ID NO:32)MTVTYAHEPFTDFTEAKNKTAFGESLAFVNTQLGKHYPLVINGEKIETDRKIISINPANKEEIIGYASTADQELAEKAMQAALQAFDSWKKQRPEHRANILFKAAAILRRRKHEFSSYLVKEAGKPWKEADADTAEAIDFLEFYARQMLKLKEGAPVKSAAGEVNQYHYEALGVGIVISPFNFPLAIMAGTAVAAIVTGNTILLKPADAAPVVAAKFVEVMEEAGLPNGVLNYIPGDGAEIGDFLVEHPKTRFVSFTGSRAVGCRIYERMKVQPGQKWLKRVIAEMGGKDTVLVDKDADLDLAASSIVYSAFGYSGQKCSAGSRAVIHQDVYDEVVEKAVALTKTLTVGNPEDPDTYMGPVIHEASYNKVMKYIEIGKSEGKLLAGGEGDDSKGYFIQPTIFADVDENARLMQEEIFGPVVAICKARDFDHMLEIANNTEYGLTGALLTKNRAHIERAREDFHVGNLYFNRGCTGAIVGYQPFGGFNMSGTDSKAGGPDY LILHMQAKTTSEAF.

Additionally, the coding region is found at about 3877991-3879535 bp ofthe B. subtilis 168 chromosome.

The rocD coding sequence of the rocD protein (ornithineaminotransferase) of B. subtilis 168 is shown below: (SEQ ID NO:33)ATGACAGCTTTATCTAAATCCAAAGAAATTATTGATCAGACGTCTCATTACGGAGCCAACAATTATCACCCGCTCCCGATTGTTATTTCTGAAGCGCTGGGTGCTTGGGTAAAGGACCCGGAAGGCAATGAATATATGGATATGCTGAGTGCTTACTCTGCGGTAAACCAGGGGCACAGACACCCGAAAATCATTCAGGCATTAAAGGATCAGGCTGATAAAATCACCCTCACGTCACGCGCGTTTCATAACGATCAGCTTGGGCCGTTTTACGAAAAAACAGCTAAACTGACAGGCAAAGAGATGATTCTGCCGATGAATACAGGAGCCGAAGCGGTTGAATCCGCGGTGAAAGCGGCGAGACGCTGGGCGTATGAAGTGAAGGGCGTAGCTGACAATCAAGCGGAAATTATCGCATGTGTCGGGAACTTCCACGGCCGCACGATGCTGGCGGTATCTCTTTCTTCTGAAGAGGAATATAAACGAGGATTCGGCGCGATGCTTCCAGGAATCAAACTCATTCCTTACGGCGATGTGGAAGCGCTTCGACAGGCCATTACGCCGAATACAGCGGCATTCTTGTTTGAACCGATTCAAGGCGAAGCGGGCATTGTGATTCCGCCTGAAGGATTTTTACAGGAAGCGGCGGCGATTTGTAAGGAAGAGAATGTCTTGTTTATTGCGGATGAAATTCAGACGGGTCTCGGACGTACAGGCAAGACGTTTGCCTGTGACTGGGACGGCATTGTTCCGGATATGTATATCTTGGGCAAAGCGCTTGGCGGCGGTGTGTTCCCGATCTCTTGCATTGCGGCGGACCGCGAGATCCTAGGCGTGTTTAACCCTGGCTCACACGGCTCAACATTTGGTGGAAACCCGCTTGCATGTGCAGTGTCTATCGCTTCATTAGAAGTGCTGGAGGATGAAAAGCTGGCGGATCGTTCTCTTGAACTTGGTGAATACTTTAAAAGCGAGCTTGAGAGTATTGACAGCCCTGTCATTAAAGAAGTCCGCGGCAGAGGGCTGTTTATCGGTGTGGAATTGACTGAAGCGGCACGTCCGTATTGTGAGCGTTTGAAGGAAGAGGGACTTTTATGCAAGGAAACGCATGATACAGTCATTCGTTTTGCACCGCCATTAATCATTTCCAAAGAGGACTTGGATTGGGCGATAGAGAAAATTAAGCACGTGCTGCGAAAC GCA.

The deduced amino acid sequence of the RocD protein is: (SEQ ID NO:34)MTALSKSKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEAARPYCERLKEEGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVLRN A.

Additionally, the coding region is found at about 4143328-4144530 bp ofthe B. subtilis 168 chromosome.

The rocF coding sequence of the rocF protein (arginase) of B. subtilis168 is shown below: (SEQ ID NO:35)ATGGATAAAACGATTTCGGTTATTGGAATGCCAATGGATTTAGGACAAGCACGACGCGGAGTGGATATGGGCCCGAGTGCCATCCGGTACGCTCATCTGATCGAGAGGCTGTCAGACATGGGGTATACGGTTGAAGATCTCGGTGACATTCCGATCAATCGCGAAAAAATCAAAAATGACGAGGAACTGAAAAACCTGAATTCCGTTTTGGCGGGAAATGAAAAACTCGCGCAAAAGGTCAACAAAGTCATTGAAGAGAAAAAATTCCCGCTTGTCCTGGGCGGTGACCACAGTATTGCGATCGGCACGCTTGCAGGCACAGCGAAGCATTACGATAATCTCGGCGTCATCTGGTATGACGCGCACGGCGATTTGAATACACTTGAAACTTCACCATCGGGCAATATTCACGGCATGCCGCTCGCGGTCAGCCTAGGCATTGGCCACGAGTCACTGGTTAACCTTGAAGGCTACGCGCCTAAAATCAAACCGGAAAACGTCGTCATCATTGGCGCCCGGTCACTTGATGAAGGGGAGCGCAAGTACATTAAGGAAAGCGGCATGAAGGTGTACACAATGCACGAAATCGATCGTCTTGGCATGACAAAGGTCATTGAAGAAACCCTTGATTATTTATCAGCATGTGATGGCGTCCATCTGAGCCTTGATCTGGACGGACTTGATCCGAACGACGCACCGGGTGTCGGAACCCCTGTCGTCGGCGGCATCAGCTACCGGGAGAGCCATTTGGCTATGGAAATGCTGTATGACGCAGGCATCATTACCTCAGCCGAATTCGTTGAGGTTAACCCGATCCTTGATCACAAAAACAAAACGGGCAAAACAGCAGTAGAGCTCGTAGAATCCCTGTTAGGGAAGAAGCTGCTG.

The deduced amino acid sequence of the RocF protein: (SEQ ID NO:36)MDKTISVIGMPMDLGQARRGVDMGPSAIRYAHLIERLSDMGYTVEDLGDIPINREKIKNDEELKNLNSVLAGNEKLAQKVNKVIEEKKFPLVLGGDHSIAIGTLAGTAKHYDNLGVIWYDAHGDLNTLETSPSGNIHGMPLAVSLGIGHESLVNLEGYAPKIKPENVVIIGARSLDEGERKYIKESGMKVYTMHEIDRLGMTKVIEETLDYLSACDGVHLSLDLDGLDPNDAPGVGTPVVGGISYRESHLAMEMLYDAGIITSAEFVEVNPILDHKNKTGKTAVELVESLLGKKLL.

Additionally, the coding region is found at about 4140738-4141625 bp ofthe B. subtilis 168 chromosome.

The Tdh coding sequence of the Tdh protein (threonine 3-dehydrogenase)of B. subtilis 168 is shown below: (SEQ ID NO:37)ATGCAGAGTGGAAAGATGAAAGCTCTAATGAAAAAGGACGGGGCGTTCGGTGCTGTGCTGACTGAAGTTCCCATTCCTGAGATTGATAAACATGAAGTCCTCATAAAAGTGAAAGCCGCTTCCATATGCGGCACGGATGTCCACATTTATAATTGGGATCAATGGGCACGTCAGAGAATCAAAACACCCTATGTTTTCGGCCATGAGTTCAGCGGCATCGTAGAGGGCGTGGGAGAGAATGTCAGCAGTGTAAAAGTGGGAGAGTATGTGTCTGCGGAAACACACATTGTCTGTGGTGAATGTGTCCCTTGCCTAACAGGAAAATCTCATGTGTGTACCAATACTGCTATAATCGGAGTGGACACGGCAGGCTGTTTTGCGGAGTATGTAAAAGTTCCAGCTGATAACATTTGGAGAAATCCCGCTGATATGGACCCGTCGATTGCTTCCATTCAAGAGCCTTTAGGAAATGCAGTTCATACCGTACTCGAGAGCCAGCCTGCAGGAGGAACGACTGCAGTCATTGGATGCGGACCGATTGGTCTTATGGCTGTTGCGGTTGCAAAAGCAGCAGGAGCTTCTCAGGTGATAGCGATTGATAAGAATGAATACAGGCTGAGGCTTGCAAAACAAATGGGAGCGACTTGTACTGTTTCTATTGAAAAAGAAGACCCGCTCAAAATTGTAAGCGCTTTAACGAGTGGAGAAGGAGCAGATCTTGTTTGTGAGATGTCGGGCCATCCCTCAGCGATTGCCCAAGGTCTTGCGATGGCTGCGAATGGCGGAAGATTTCATATTCTCAGCTTGCCGGAACATCCGGTGACAATTGATTTGACGAATAAAGTGGTATTTAAAGGGCTTACCATCCAAGGAATCACAGGAAGAAAAATGTTTTCAACATGGCGCCAGGTGTCTCAGTTGATCAGTTCAAACATGATCGATCTTGCACCTGTTATTACCCATCAGTTTCCATTAGAGGAGTTTGAAAAAGGTTTCGAACTGATGAGAAGCGGGCAGTGCGGAAAAGTAATTTTAATTCCA.

The deduced amino acid sequence of the Tdh protein is: (SEQ ID NO:38)MQSGKMKALMKKDGAFGAVLTEVPIPEIDKHEVLIKVKAASICGTDVHIYNWDQWARQRIKTPYVFGHEFSGIVEGVGENVSSVKVGEWSAETHIVCGECVPCLTGKSHVCTNTAIIGVDTAGCFAEYVKVPADNIWRNPADMDPSIASIQEPLGNAVHTVLESQPAGGTTAVIGCGPIGLMAVAVAKAAGASQVIAIDKNEYRLRLAKQMGATCTVSIEKEDPLKIVSALTSGEGADLVCEMSGHPSAIAQGLAMAANGGRFHILSLPEHPVTIDLTNKVVFKGLTIQGITGRKMFSTWRQVSQLISSNMIDLAPVITHQFPLEEFEKGFELMRSGQCGKVILIP.

Additionally, the coding region is found at about 1769731-1770771 bp ofthe B. subtilis 168 chromosome.

The coding sequences for the tryptophan operon regulatory region andgenes trpE (SEQ ID NO:48), trpD (SEQ ID NO:46), trpC (SEQ ID NO:44),trpF (SEQ ID NO:50), trpB (SEQ ID NO:42), and trpA (SEQ ID NO:40) areshown below. The operon regulatory region is underlined. The trpE start(ATG) is shown in bold, followed as well by the trpD, trpC trpF, trpB,and trpA starts (also indicated in bold, in the order shown). (SEQ IDNO:39) TAATACGATAAGAACAGCTTAGAAATACACAAGAGTGTGTATAAAGCAATTAGAATGAGTTGAGTTAGAGAATAGGGTAGCAGAGAATGAGTTTAGTTGAGCTGAGACATTATGTTTATTCTACCCAAAAGAAGTCTTTCTTTTGGGTTTATTTGTTATATAGTATTTTATCCTCTCATGCCATCTTCTCATTCTCCTTG CCATAAGGAGTGAGAGCAATGAATTTCCAATCAAACATTTCCGCATTTTTAGAGGACAGCTTGTCCCACCACACGATACCGATTGTGGAGACCTTCACAGTCGATACACTGACACCCATTCAAATGATAGAGAAGCTTGACAGGGAGATTACGTATCTTCTTGAAAGCAAGGACGATACATCCACTTGGTCCAGATATTCGTTTATCGGCCTGAATCCATTTCTCACAATTAAAGAAGAGCAGGGCCGTTTTTCGGCCGCTGATCAGGACAGCAAATCTCTTTACACAGGAAATGAACTAAAAGAAGTGCTGAACTGGATGAATACCACATACAAAATCAAAACACCTGAGCTTGGCATTCCTTTTGTCGGCGGAGCTGTCGGGTACTTAAGCTATGATATGATCCCGCTGATTGAGCCTTCTGTTCCTTCGCATACCAAAGAAACAGACATGGAAAAGTGTATGCTGTTTGTTTGCCGGACATTAATTGCGTATGATCATGAAACCAAAAACGTCCACTTTATCCAATATGCAAGGCTCACTGGAGAGGAAACAAAAAACGAAAAAATGGATGTATTCCATCAAAATCATCTGGAGCTTCAAAATCTCATTGAAAAAATGATGGACCAAAAAAACATAAAAGAGCTGTTTCTTTCTGCTGATTCATACAAGACACCCAGCTTTGAGACAGTATCTTCTAATTATGAAAAATCGGCTTTTATGGCTGATGTAGAAAAAATCAAAAGCTATATAAAAGCAGGCGATATCTTCCAGGGTGTTTTATCACAAAAATTTGAGGTGCCGATAAAAGCAGATGCTTTTGAGTTATACCGAGTGCTTAGGATCGTCAATCCTTCGCCGTATATGTATTATATGAAACTGCTAGACAGAGAAATAGTCGGCAGCTCTCCGGAACGGTTAATACACGTTCAAGACGGGCACTTAGAAATCCATCCGATTGCCGGTACGAGAAAACGCGGTGCAGACAAAGCTGAAGATGAGAGACTGAAGGTTGAGCTCATGAAGGATGAAAAAGAAAAAGCGGAGCATTACATGCTCGTTGATCTTGCCCGAAACGATATCGGCAGAGTAGCAGAGTATGGTTCTGTTTCTGTGCCGGAGTTCACAAAAATTGTTTCCTTTTCACATGTCATGCACATTATCTCGGTGGTTACAGGCCGATTGAAAAAAGGGGTTCATCCTGTCGATGCACTGATGTCTGCTTTCCCGGCGGGGACTTTAACAGGCGCACCCAAAATCCGTGCCATGCAGCTTTTGCAAGAACTCGAGCCAACACCGAGAGAGACATACGGAGGGTGTATTGCCTACATTGGGTTTGACGGGAATATCGACTCTTGTATTACGATTCGCACGATGAGTGTAAAGAACGGTGTTGCATCGATACAGGCAGGTGCTGGCATTGTTGCTGATTCTGTTCCGGAAGCCGAATACGAAGAAAGCTGTAATAAAGCCGGTGCGCTGCTGAAAACGATTCATATTGCAGAAGACATGTTTCATAGCAAGGAGGATAAAGCTGATGAACAGATTTCTACAATTGTGCGTTGACGGAAAAACCCTTACTGCCGGTGAGGCTGAAACGCTGATGAATATGATGATGGCAGCGGAAATGACTCCTTCTGAAATGGGGGGGATATTGTCAATTCTTGCTCATCGGGGGGAGACGCCAGAAGAGCTTGCGGGTTTTGTGAAGGCAATGCGGGCACACGCTCTTACAGTCGATGGACTTCCTGATATTGTTGATACATGCGGAACAGGGGGAGACGGTATTTCCACTTTTAATATCTCAACGGCCTCGGCAATTGTTGCCTCGGCAGCTGGTGCGAAAATCGCTAAGCATGGCAATCGCTCTGTCTCTTCTAAAAGCGGAAGCGCTGATGTTTTAGAGGAGCTAGAGGTTTCTATTCAAACCACTCCCGAAAAGGTCAAAAGCAGCATTGAAACAAACAACATGGGATTTCTTTTTGCGCCGCTTTACCATTCGTCTATGAAACATGTAGCAGGTACTAGAAAAGAGCTAGGTTTCAGAACGGTATTTAATCTGCTTGGGCCGCTCAGCAATCCTTTACAGGCGAAGCGTCAGGTGATTGGGGTCTATTCTGTTGAAAAAGCTGGACTGATGGCAAGCGCACTGGAGACGTTTCAGCCGAAGCACGTTATGTTTGTATCAAGCCGTGACGGTTTAGATGAGCTTTCAATTACAGCACCGACCGACGTGATTGAATTAAAGGACGGAGAGCGCCGGGAGTATACCGTTTCACCCGAAGATTTCGGTTTCACAAATGGCAGACTTGAAGATTTACAGGTGCAGTCTCCGAAAGAGAGCGCTTATCTCATTCAGAATATTTTTGAAAATAAAAGCAGCAGTTCCGCTTTATCTATTACGGCTTTTAATGCGGGTGCTGCGATTTACACGGCGGGAATTACCGCCTCACTGAAGGAAGGAACGGAGCTGGCGTTAGAGACGATTACAAGCGGAGGCGCTGCCGCGCAGCTTGAACGACTAAAGCAGAAAGAGGAAGAGATCTATGCTTGAAAAAATCATCAAACAAAAGAAAGAAGAAGTGAAAACACTGGTTCTGCCGGTAGAGCAGCCTTTCGAGAAACGTTCATTTAAGGAGGCGCCGGCAAGCCCGAATCGGTTTATCGGGTTGATTGCCGAAGTGAAGAAAGCATCGCCGTCAAAAGGGCTTATTAAAGAGGATTTTGTACCTGTGCAGATTGCAAAAGACTATGAGGCTGCGAAGGCAGATGCGATTTCCGTTTTAACAGACACCCCGTTTTTTCAAGGGGAAAACAGCTATTTATCAGACGTAAAGCGTGCTGTTTCGATTCCTGTACTTAGAAAAGATTTTATTATTGATTCTCTTOAAGTAGAGGAATCAAGAAGAATCGGAGCGGATGCCATATTGTTAATCGGCGAGGTGCTTGATCCCTTACACCTTCATGAATTATATCTTGAAGCAGGTGAAAAGGGGATGGACGTGTTAGTGGAGGTTCATGATGCATCAACGCTAGAACAAATATTGAAAGTGTTCACACCCGACATTCTCGGCGTAAATAATCGAAACCTAAAAACGTTTGAAACATCTGTAAAGCAGACAGAACAAATCGCATCTCTCGTTCCGAAAGAATCCTTGCTTGTCAGCGAAAGCGGAATCGGTTCTTTAGAACATTTAACATTTGTCAATGAACATGGGGCGCGAGCTGTACTTATCGGTGAATCATTGATGAGACAAACTTCTCAGCGTAAAGCAATCCATGCTTTGTTTAGGGAGTGAGGTTGTGAAGAAACCGGCATTAAAATATTGCGGTATTCGGTCACTAAAGGATTTGCAGCTTGCGGCGGAATCACAGGCTGATTACCTAGGATTTATTTTTGCTGAAAGCAAACGAAAAGTATCTCCGGAAGATGTGAAAAAATGGCTGAACCAAGTTCGTGTCGAAAAACAGGTTGCAGGTGTTTTTGTTAATGAATCAATAGAGACGATGTCACGTATTGCCAAGAGCTTGAAGCTCGACGTCATTCAGCTTCACGGTGATGAAAAACCGGCGGATGTCGCTGCTCTTCGCAAGCTGACAGGCTGTGAAATATGGAAGGCGCTTCACCATCAAGATAACACAACTCAAGAAATAGCCCGCTTTAAAGATAATGTTGACGGCTTTGTGATTGATTCATCTGTAAAAGGGTCTAGAGGCGGAACTGGTGTTGCATTTTCTTGGGACTGTGTGCCGGAATATCAGCAGGCGGCTATTGGTAAACGCTGCTTTATCGCTGGCGGCGTGAATCCGGATAGCATCACACGCCTATTGAAATGGCAGCCAGAAGGAATTGACCTTGCCAGCGGAATTGAAAAAAACGGACAAAAAGATCAGAATCTGATGAGGCTTTTAGAAGAAAGGATGAACCGATATGTATCCATATCCGAATGAAATAGGCAGATACGGTGATTTTGGCGGAAAGTTTGTTCCGGAAACACTCATGCAGCCGTTAGATGAAATACAAACAGCATTTAAACAAATCAAGGATGATCCCGCTTTTCGTGAAGAGTATTATAAGCTGTTAAAGGACTATTCCGGACGCCCGACTGCATTAACATACGCTGATCGAGTCACTGAATACTTAGGCGGCGCGAAAATCTATTTGAAACGAGAAGATTTAAACCATACAGGTTCTCATAAAATCAATAATGCGCTAGGTCAAGCGCTGCTTGCTAAAAAAATGGGCAAAACGAAAATCATTGCTGAAACCGGTGCCGGCCAGCATGGTGTTGCCGCTGCAACAGTTGCAGCCAAATTCGGCTTTTCCTGTACTGTGTTTATGGGTGAAGAGGATGTTGCCCGCCAGTCTCTGAACGTTTTCCGCATGAAGCTTCTTGGAGCGGAGGTAGTGCCTGTAACAAGCGGAAACGGAACATTGAAGGATGCCACAAATGAGGCGATCCGGTACTGGGTTCAGCATTGTGAGGATCACTTTTATATGATTGGATCAGTTGTCGGCCCGCATCCTTATCCGCAAGTGGTCCGTGAATTTCAAAAAATGATCGGAGAGGAAGCGAAGGATCAGTTGAAACGTATTGAAGGCACTATGCCTGATAAAGTAGTGGCATGTGTAGGCGGAGGAAGCAATGCGATGGGTATGTTTCAGGCATTTTTAAATGAAGATGTTGAACTGATCGGCGCTGAAGCAGCAGGAAAAGGAATTGATACACCTCTTCATGCCGCCACTATTTCGAAAGGAACCGTAGGGGTTATTCACGGTTCATTGACTTATCTCATTCAGGATGAGTTCGGGCAAATTATTGAGCCCTACTCTATTTCAGCCGGTCTCGACTATCCTGGAATCGGTCCGGAGCATGCATATTTGCATAAAAGCGGCCGTGTCACTTATGACAGTATAACCGATGAAGAAGCGGTGGATGCATTAAAGCTTTTGTCAGAAAAAGAGGGGATTTTGCCGGCAATCGAATCTGCCCATGCGTTAGCGAAAGCATTCAAACTCGCCAAAGGAATGGATCGCGGTCAACTCATTCTCGTCTGTTTATCAGGCCGGGGAGACAAGGATGTCAACACATTAATGAATGTATTGGAAGAAGAGGTGAAAGCCCATGTTTAAATTGGATCTTCAACCATCAGAAAAATTGTTTATCCCGTTTATTACGGCGGGCGATCCAGTTCCTGAGGTTTCGATTGAACTGGCGAAGTCACTCCAAAAAGCAGGCGCCACAGCATTGGAGCTTGGTGTTGCATACTCTGACCCGCTTGCAGACGGTCCGGTGATCCAGCGGGCTTCAAAGCGGGCGCTTGATCAAGGAATGAATATCGTAAAGGCAATCGAATTAGGCGGAGAAATGAAAAAAAACGGAGTGAATATTCCGATTATCCTCTTTACGTATTATAATCCTGTGTTACAATTGAACAAAGAATACTTTTTCGCTTTACTGCGGGAAAATCATATTGACGGTCTGCTTGTTCCGGATCTGCCATTAGAAGAAAGCAACAGCCTTCAAGAGGAATGTAAAAGCCATGAGGTGACGTATATTTCTTTAGTTGCGCCGACAAGCGAAAGCCGTTTGAAAACCATTATTGAACAAGCCGAGGGGTTCGTCTACTGTGTATCTTCTCTGGGTGTGACCGGTGTCCGCAATGAGTTCAATTCATCCGTGTACCCGTTCATTCGTACTGTGAAGAATCTCAGCACTGTTCCGGTTGCTGTAGGGTTCGGTATATCAAACCGTGAACAGGTCATAAAGATGAATGAAATTAGTGACGGTGTCGTAGTGGGAAGTGCGCTCGTCAGAAAAATAGAAGAATTAAAGGACCGGCTCATCAGCGCTGAAACGAGAAATCAGGCGCTGCAGGAGTTTGAGGATTATGCAATGGCGTTTAGCGGCTTGTACAGTTTAAAA.

The deduced TrpA protein (tryptophan synthase (alpha subunit)) sequenceis: (SEQ ID NO:41) MFKLDLQPSEKLFIPFITAGDPVPEVSIELAKSLQKAGATALELGVAYSDPLADGPVIQRASKRALDQGMNIVKAIELGGEMKKNGVNIPIILFTYYNPVLQLNKEYFFALLRENHIDGLLVPDLPLEESNSLQEECKSHEVTYISLVAPTSESRLKTIIEQAEGFVYCVSSLGVTGVRNEFNSSVYPFIRTVKNLSTVPVAVGFGISNREQVIKMNEISDGVWGSALVRKIEELKDRLISAETRNQALQ EFEDYAMAFSGLYSLK.

The deduced TrpB protein (tryptophan synthase (beta subunit)) sequenceis: (SEQ ID NO:43) MYPYPNEIGRYGDFGGKFVPETLMQPLDEIQTAFKQIKDDPAFREEYYKLLKDYSGRPTALTYADRVTEYLGGAKIYLKREDLNHTGSHKINNALGQALLAKKMGKTKIIAETGAGQHGVAAATVAAKFGFSCTVFMGEEDVARQSLNVFRMKLLGAEWPVTSGNGTLKDATNEAIRYWVQHCEDHFYMIGSVVGPHPYPQWREFQKMIGEEAKDQLKRIEGTMPDKVVACVGGGSNAMGMFQAFLNEDVELIGAEAAGKGIDTPLHAATISKGTVGVIHGSLTYLIQDEFGQIIEPYSISAGLDYPGIGPEHAYLHKSGRVTYDSITDEEAVDALKLLSEKEGILPAIESAHALAKAFKLAKGMDRGQLILVCLSGRGDKDVNTLMNVLEEEVKAHV.

The deduced TrpC protein indol-3-glycerol phosphate synthase) sequenceis: (SEQ ID NO:45) MLEKIIKQKKEEVKTLVLPVEQPFEKRSFKEAPASPNRFIGLIAEVKKASPSKGLIKEDFVPVQIAKDYEAAKADAISVLTDTPFFQGENSYLSDVKRAVSIPVLRKDFIIDSLQVEESRRIGADAILLIGEVLDPLHLHELYLEAGEKGMDVLVEVHDASTLEQILKVFTPDILGVNNRNLKTFETSVKQTEQIASLVPKESLLVSESGIGSLEHLTFVNEHGARAVLIGESLMRQTSQRKAIHALFRE .

The deduced TrpD protein (anthranilate phosphoribosyltransferase)sequence is: (SEQ ID NO:47)MNRFLQLCVDGKTLTAGEAETLMNMMMAAEMTPSEMGGILSILAHRGETPEELAGFVKAMRAHALTVDGLPDIVDTCGTGGDGISTFNISTASAIVASAAGAKIAKHGNRSVSSKSGSADVLEELEVSIQTTPEKVKSSIETNNMGFLFAPLYHSSMKHVAGTRKELGFRTVFNLLGPLSNPLQAKRQVIGVYSVEKAGLMASALETFQPKHVMFVSSRDGLDELSITAPTDVIELKDGERREYTVSPEDFGFTNGRLEDLQVQSPKESAYLIQNIFENKSSSSALSITAFNAGAAIYTAGITASLKEGTELALETITSGGAAAQLERLKQKEEEIYA.

The deduced TrpE protein (anthranilate synthase) sequence is: (SEQ IDNO:49) MNFQSNISAFLEDSLSHHTIPIVETFTVDTLTPIQMIEKLDREITYLLESKDDTSTWSRYSFIGLNPFLTIKEEQGRFSAADQDSKSLYTGNELKEVLNWMNTTYKIKTPELGIPFVGGAVGYLSYDMIPLIEPSVPSHTKETDMEKCMLFVCRTLIAYDHETKNVHFIQYARLTGEETKNEKMDVFHQNHLELQNLIEKMMDQKNIKELFLSADSYKTPSFETVSSNYEKSAFMADVEKIKSYIKAGDIFQGVLSQKFEVPIKADAFELYRVLRIVNPSPYMYYMKLLDREIVGSSPERLIHVQDGHLEIHPIAGTRKRGADKAEDERLKVELMKDEKEAEHYMLVDLARNDIGRVAEYGSVSVPEFTKIVSFSHVMHIISWTGRLKKGVHPVDALMSAFPAGTLTGAPKIRAMQLLQELEPTPRETYGGCIAYIGFDGNIDSCITIRTMSVKNGVASIQAGAGIVADSVPEAEYEESCNKAGALLKTIHIAEDMFHSK EDKADEQISTIVR.

The deduced TrpF protein (phosphoribosyl anthranilate isomerase)sequence is: (SEQ ID NO:51)MKKPALKYCGIRSLKDLQLAAESQADYLGFIFAESKRKVSPEDVKKWLNQVRVEKQVAGVFVNESIETMSRIAKSLKLDVIQLHGDEKPADVAALRKLTGCEIWKALHHQDNTTQEIARFKDNVDGFVIDSSVKGSRGGTGVAFSWDCVPEYQQAAIGKRCFIAGGVNPDSITRLLKWQPEGIDLASGIEKNGQKDQNLM RLLEERMNRYVSISE.

Additionally, the coding region is found at about 2370707 bp to 2376834bp (first bp=2376834; last bp=2370707) bp of the B. subtilis 168chromosome.

The ycgM coding sequence of the ycgM protein (similar to prolineoxidase) of B. subtilis 168 is shown below: (SEQ ID NO:52)GTGATCACAAGAGATTTTTTCTTATTTTTATCCAAAAGCGGCTTTCTCAATAAAATGGCGAGGPACTGGGGAAGTCGGGTAGCAGCGGGTAAAATTATCGGCGGGAATGACTTTAACAGTTCAATCCCGACCATTCGACAGCTTAACAGCCAAGGCTTGTCAGTTACTGTCGATCATTTAGGCGAGTTTGTGAACAGCGCCGAGGTCGCACGGGAGCGTACGGAAGAGTGCATTCAAACCATTGCGACCATCGCGGATCAGGAGCTGAACTCACACGTTTCTTTAAAAATGACGTCTTTAGGTTTGGATATAGATATGGATTTGGTGTATGAAAATATGACAAAAATCCTTCAGACGGCCGAGAAACATAAAATCATGGTCACCATTGACATGGAGGACGAAGTCAGATGCCAGAAAACGCTTGATATTTTCAAAGATTTCAGAAAGAAATACGAGCATGTGAGCACAGTGCTGCAAGCCTATCTGTACCGGACGGAAAAAGACATTGACGATTTGGATTCTTTAAACCCGTTCCTTCGCCTTGTAAAAGGAGCTTATAAAGAATCAGAAAAAGTAGCTTTCCCGGAGAAAAGCGATGTCGATGAAAATTACAAAAAAATCATCCGAAAGCAGCTCTTAAACGGTCACTATACAGCGATTGCCACACATGACGACAAAATGATCGACTTTACAAAGCAGCTTGCCAAGGAACATGGCATTGCCMTGACAAGTTTGAATTTCAGATGCTGTACGGCATGCGGTCGCAAACCCAGCTCAGCCTCGTAAAAGAAGGTTATAACATGAGAGTCTACCTGCCATACGGCGAGGATTGGTACGGCTACTTTATGAGACGCCTTGCAGAACGTCCGTCAAACATTGCATTTGCTTTCAAAGGAATGA CAAAGAAG.

The deduced amino acid sequence of the YcgM protein is: (SEQ ID NO:53)MITRDFFLFLSKSGFLNKMARNWGSRVAAGKIIGGNDFNSSIPTIRQLNSQGLSVTVDHLGEFVNSAEVARERTEECIQTIATIADQELNSHVSLKMTSLGLDIDMDLVYENMTKILQTAEKHKIMVTIDMEDEVRCQKTLDIFKDFRKKYEHVSTVLQAYLYRTEKDIDDLDSLNPFLRLVKGAYKESEKVAFPEKSDVDENYKKIIRKQLLNGHYTAIATHDDKMIDFTKQLAKEHGIANDKFEFQMLYGMRSQTQLSLVKEGYNMRVYLPYGEDWYGYFMRRLAERPSNIAFAFKGM TKK.

Additionally, the coding region is found at about 344111-345019 bp ofthe B. subtilis 168 chromosome.

The ycgN coding sequence of the ycgN protein (similar to1-pyrroline-5-carboxylate dehydrogenase) of B. subtilis 168 is shownbelow: (SEQ ID NO:54) ATGACAACACCTTACMACACGAGCCATTCACAAATTTCCAAGATCAAAACTACGTGGAAGCGTTTAAAAAAGCGCTTGCGACAGTAAGCGAATATTTAGGAAAAGACTATCCGCTTGTCATTAACGGCGAGAGAGTGGAAACGGAAGCGAAAATCGTTTCAATCAACCCAGCTGATAAAGAAGAAGTCGTCGGCCGAGTGTCAAAAGCGTCTCAAGAGCACGCTGAGCAAGCGATTCAAGCGGCTGCAAAAGCATTTGAAGAGTGGAGATACACGTCTCCTGAAGAGAGAGCGGCTGTCCTGTTCCGCGCTGCTGCCAAAGTCCGCAGAAGAAAACATGAATTCTCAGCTTTGCTTGTGAAAGAAGCAGGAAAGCCTTGGAACGAGGCGGATGCCGATACGGCTGAAGCGATTGACTTCATGGAGTATTATGCACGCCAATGATCGAACTGGCAAAAGGCAAACCGGTCAACAGCCGTGAAGGCGAGAAAAACCAATATGTATACACGCCGACTGGAGTGACAGTCGTTATCCCGCCTTGGAACTTCTTGAAGCGATCATGGCAGGCACAACAGTGGCGCCGATCGTTACTGGAAACACAGTGGTTCTGAACCTGCGAGTGCTACACCTGTTATTGCAGCAAAATTTGTTGAGGTGCTTGAAGAGTCCGGATTGCCAAAAGGCGTAGTCAACTTTGTTCCGGGAAGCGGATCGGAAGTAGGCGACTATCTTGTTGACCATCCGAAAACAAGCCTTATCACATTTACGGGATCAAGAGAAGTTGGTACGAGAATTTTCGAACGCGCGGCGAAGGTTCAGCCGGGCCAGCAGCATTTAAAGCGTGTCATCGCTGAAATGGGCGGTAAAGATACGGTTGTTGTTGATGAGGATGCGGACAAAGAATTAGCGGCTCAATCGATCTTTACTTCAGCATTCGGCTTTGCGGGACAAAAATGCTCTGCAGGTTCACGTGCAGTAGTTCATGAAAAAGTGTATGATCAAGTAUAGAGCGTGTCATTGAAATTACGGAATCAAAAGTAACAGCTAAACCTGACAGTGCAGATGTTTATATGGGACCTGTCATTGACCAAGGTTCTTATAAAATTATGAGCTATTGAGATCGGAAAACAGGAAGGGCGTTTAGTAAGCGGCGGTACTGGTGATGATTCGAAAGGATACTTCATCAAACCGACGATCTTCGCTGACCTTGATCCGAAAGCAAGACTCATGCAGGAAGAAAATTTTCGGACCTGTCGTTGCATTTTGTAAAGTGTCAGACTTTGATGAAGCTTTAGAAGTGGCAAACAATACTGAATATGGTTTGACAGGCGCGGTTATCACAAACAACCGCAAGCACATCGAGCGTGCGAAACAGGAATTCCATGTCGGAAACCTATACTTCAACCGCAACTGTACAGGTGCTATCGTCGGCTACCATCCGTTTGGCGGCTTCTGTCGGGAACGGAAACAAAGCAGGCGGGCCGGATTACTTGGCTCTGCATATGCAAAAAGGCAATCAGTGAAATGTTC.

The deduced amino acid sequence of YcgN protein is: (SEQ ID NO:55)MTTPYKHEPFTNFQDQNYVEAFKKALATVSEYLGKDYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGSEVGDYLVDHPKTSLITFTGSREVGTRIFERAAQPGQQHLKRVIAEMGGKDTWVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLA LHMQAKTISEMF.

Additionally, the coding region is found at about 345039-346583 bp ofthe B. subtilis 168 chromosome.

The sigD coding sequence of the sigD protein (RNA polymerase flagella,motility, chemotaxis and autolysis sigma factor) of B. subtilis 168 isshown below: (SEQ ID NO:56)ATGCAATCCTTGAATTATGAAGATCAGGTGCTTTGGACGCGCTGGAAAGAGTGGAAAGATCCTAAAGCCGGTGACGACTTAATGCGCCGTTACATGCCGCTTGTCACATATCATGTAGGCAGAATTTCTGTCGGACTGCCGAAATCAGTGCATAAAGACGATCTTATGAGCCTTGGTATGCTTGGTTTATATGATGCCCTTGAAAAATTTGACCCCAGCCGGGACTTAAAATTTGATACCTACGCCTCGTTTAGAATTCGCGGCGCAATCATAGACGGGCTTCGTAAAGAAGATTGGCTGCCCAGAACCTCGCGCGAAAAAACAAAAAAGGTTGAAGCAGCAATTGAAAAGCTTGAACAGCGGTATCTTCGGAATGTATCGCCCGCGGAAATTGCAGAGGAACTCGGAATGACGGTACAGGATGTCGTGTCAACAATGAATGAAGGTTTTTTTGCAAATCTGCTGTCAATTGATGAAAAGCTCCATGATCAAGATGACGGGGAAAACATTCAAGTCATGATCAGAGATGACAAAAATGTTCCGCCTGAAGAAAAGATTATGAAGGATGAACTGATTGCACAGCTTGCGGAAAAAATTCACGAACTCTCTGAAAAAGAACAGCTGGTTGTCAGTTTGTTCTACAAAGAGGAGTTGACACTGACAGAAATCGGACAAGTATTAAATCTTTCTACGTCCCGCATATCTCAGATCCATTCAAAGGCATTATTTAAATTAAAGAATCTGCTGGAA AAAGTGATACAA.

The deduced amino acid sequence of the SigD is: (SEQ ID NO:57)MQSLNYEDQVLWTRWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRTSREKTKKVEAAIEKLEQRYLRNVSPAEIAEELGMTVQDWSTMNEGFFANLLSIDEKLHDQDDGENIQVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLWSLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKNLLEKV IQ.

Additionally, the coding region is found at about 1715786-1716547 bp ofthe B. subtilis 168 chromosome.

As indicated above, it is contemplated that inactivated analogous genesfound in other Bacillus hosts will find use in the present invention.

In some preferred embodiments, the host cell is a member of the genusBacillus, while in some embodiments, the Bacillus strain of interest isalkalophilic. Numerous alkalophilic Bacillus strains are known (Seee.g., U.S. Pat. No. 5,217,878; and Aunstrup et al., Proc IV IFS:Ferment. Technol. Today, 299-305 [1972]). In some preferred embodiments,the Bacillus strain of interest is an industrial Bacillus strain.Examples of industrial Bacillus strains include, but are not limited toB. licheniformis, B. lentus, B. subtilis, and B. amyloliquefaciens. Inadditional embodiments, the Bacillus host strain is selected from thegroup consisting of B. lentus, B. brevis, B. stearothermophilus, B.alkalophilus, B. coagulans, B. circulans, B. pumilus, B. thuringiensis,B. clausii, and B. megaterium, as well as other organisms within thegenus Bacillus, as discussed above. In some particularly preferredembodiments, B. subtilis is used. For example, U.S. Pat. Nos. 5,264,366and 4,760,025 (RE 34,606) describe various Bacillus host strains thatfind use in the present invention, although other suitable strains arecontemplated for use in the present invention.

An industrial strain may be a non-recombinant strain of a Bacillus sp.,a mutant of a naturally occurring strain or a recombinant strain.Preferably, the host strain is a recombinant host strain wherein apolynucleotide encoding a polypeptide of interest has been introducedinto the host. A further preferred host strain is a Bacillus subtilishost strain and particularly a recombinant Bacillus subtilis hoststrain. Numerous B. subtilis strains are known, including but notlimited to 1A6 (ATCC 39085), 168 (1A01), SB19, W23, Ts85, B637, PB1753through PB1758, PB3360, JH642, 1A243 (ATCC 39,087), ATCC 21332, ATCC6051, MI113, DE100 (ATCC 39,094), GX4931, PBT 110, and PEP 211 strain(See e.g., Hoch et al., Genetics, 73:215-228 [1973]; U.S. Pat. No.4,450,235; U.S. Pat. No. 4,302,544; and EP 0134048). The use of B.subtilis as an expression host is further described by Palva et al. andothers (See, Palva et al., Gene 19:81-87 [1982]; also see Fahnestock andFischer, J. Bacteriol., 165:796-804 [1986]; and Wang et al., Gene69:39-47 [1988]).

Industrial protease producing Bacillus strains provide particularlypreferred expression hosts. In some preferred embodiments, use of thesestrains in the present invention provides further enhancements inefficiency and protease production. Two general types of proteases aretypically secreted by Bacillus sp., namely neutral (or“metalloproteases”) and alkaline (or “serine”) proteases. Serineproteases are enzymes which catalyze the hydrolysis of peptide bonds inwhich there is an essential serine residue at the active site. Serineproteases have molecular weights in the 25,000 to 30,000 range (See,Priest, Bacteriol. Rev., 41:711-753 [1977]). Subtilisin is a preferredserine protease for use in the present invention. A wide variety ofBacillus subtilisins have been identified and sequenced, for example,subtilisin 168, subtilisin BPN′, subtilisin Carlsberg, subtilisin DY,subtilisin 147 and subtilisin 309 (See e.g., EP 414279 B; WO 89/06279;and Stahl et al., J. Bacteriol., 159:811-818 [1984]). In someembodiments of the present invention, the Bacillus host strains producemutant (e.g., variant) proteases. Numerous references provide examplesof variant proteases and reference (See e.g., WO 99/20770; WO 99/20726;WO 99/20769; WO 89/06279; RE 34,606; U.S. Pat. No. 4,914,031; U.S. Pat.No. 4,980,288; U.S. Pat. No. 5,208,158; U.S. Pat. No. 5,310,675; U.S.Pat. No. 5,336,611; U.S. Pat. No. 5,399,283; U.S. Pat. No. 5,441,882;U.S. Pat. No. 5,482,849; U.S. Pat. No. 5,631,217; U.S. Pat. No.5,665,587; U.S. Pat. No. 5,700,676; U.S. Pat. No. 5,741,694; U.S. Pat.No. 5,858,757; U.S. Pat. No. 5,880,080; U.S. Pat. No. 6,197,567; andU.S. Pat. No. 6,218,165).

In yet another embodiment, a preferred Bacillus host is a Bacillus sp.that includes a mutation or deletion in at least one of the followinggenes, degU, degS, degR and degQ. Preferably the mutation is in a degUgene, and more preferably the mutation is degU(Hy)32. (See, Msadek etal., J. Bacteriol., 172:824-834 [1990]; and Olmos et al., Mol. Gen.Genet., 253:562-567 [1997]). A most preferred host strain is a Bacillussubtilis carrying a degU32(Hy) mutation. In a further embodiment, theBacillus host comprises a mutation or deletion in scoC4, (See, Caldwellet al., J. Bacteriol., 183:7329-7340 [2001]); spoIIE (See, Arigoni etal., Mol. Microbiol., 31:1407-1415 [1999]); oppA or other genes of theopp operon (See, Perego et al., Mol. Microbiol., 5:173-185 [1991]).Indeed, it is contemplated that any mutation in the opp operon thatcauses the same phenotype as a mutation in the oppA gene will find usein some embodiments of the altered Bacillus strain of the presentinvention. In some embodiments, these mutations occur alone, while inother embodiments, combinations of mutations are present. In someembodiments, an altered Bacillus of the invention is obtained from aBacillus host strain that already includes a mutation to one or more ofthe above-mentioned genes. In alternate embodiments, an altered Bacillusof the invention is further engineered to include mutation of one ormore of the above-mentioned genes.

In yet another embodiment, the incoming sequence comprises a selectivemarker located between two loxP sites (See, Kuhn and Torres, Meth. Mol.Biol., 180:175-204 [2002]), and the antimicrobial is then deleted by theaction of Cre protein. In some embodiments, this results in theinsertion of a single loxP site, as well as a deletion of native DNA, asdetermined by the primers used to construct homologous flanking DNA andantimicrobial-containing incoming DNA.

Those of skill in the art are well aware of suitable methods forintroducing polynucleotide sequences into Bacillus cells (See e.g.,Ferrari et al., “Genetics,” in Harwood et al. (ed.), Bacillus, PlenumPublishing Corp. [1989], pages 57-72; See also, Saunders et al., J.Bacteriol., 157:718-726 [1984]; Hoch et al., J. Bacteriol., 93:1925-1937[1967]; Mann et al., Current Microbiol., 13:131-135 [1986]; andHolubova, Folia Microbiol., 30:97 [1985]; for B. subtilis, Chang et al.,Mol. Gen. Genet., 168:11-115 [1979]; for B. megaterium, Vorobjeva etal., FEMS Microbiol. Lett., 7:261-263 [1980]; for B amyloliquefaciens,Smith et al., Appl. Env. Microbiol., 51:634 (1986); for B.thuringiensis, Fisher et al., Arch. Microbiol., 139:213-217 [1981]; andfor B. sphaericus, McDonald, J. Gen. Microbiol., 130:203 [1984]).Indeed, such methods as transformation including protoplasttransformation and congression, transduction, and protoplast fusion areknown and suited for use in the present invention. Methods oftransformation are particularly preferred to introduce a DNA constructprovided by the present invention into a host cell.

In addition to commonly used methods, in some embodiments, host cellsare directly transformed (i.e., an intermediate cell is not used toamplify, or otherwise process, the DNA construct prior to introductioninto the host cell). Introduction of the DNA construct into the hostcell includes those physical and chemical methods known in the art tointroduce DNA into a host cell without insertion into a plasmid orvector. Such methods include, but are not limited to calcium chlorideprecipitation, electroporation, naked DNA, liposomes and the like. Inadditional embodiments, DNA constructs are co-transformed with aplasmid, without being inserted into the plasmid. In furtherembodiments, a selective marker is deleted from the altered Bacillusstrain by methods known in the art (See, Stahl et al., J. Bacteriol.,158:411-418 [1984]; and Palmeros et al., Gene 247:255-264 [2000]).

In some embodiments, host cells are transformed with one or more DNAconstructs according to the present invention to produce an alteredBacillus strain wherein two or more genes have been inactivated in thehost cell. In some embodiments, two or more genes are deleted from thehost cell chromosome. In alternative embodiments, two or more genes areinactivated by insertion of a DNA construct. In some embodiments, theinactivated genes are contiguous (whether inactivated by deletion and/orinsertion), while in other embodiments, they are not contiguous genes.

There are various assays known to those of ordinary skill in the art fordetecting and measuring activity of intracellularly and extracellularlyexpressed polypeptides. In particular, for proteases, there are assaysbased on the release of acid-soluble peptides from casein or hemoglobinmeasured as absorbance at 280 nm or colorimetrically using the Folinmethod (See e.g., Bergmeyer et al., “Methods of Enzymatic Analysis” vol.5, Peptidases, Proteinases and their Inhibitors, Verlag Chemie, Weinheim[1984]). Other assays involve the solubilization of chromogenicsubstrates (See e.g., Ward, “Proteinases,” in Fogarty (ed.)., MicrobialEnzymes and Biotechnology, Applied Science, London, [1983], pp 251-317).Other exemplary assays include succinyl-Ala-Ala-Pro-Phe-paranitroanilide assay (SAAPFpNA) and the 2,4,6-trinitrobenzene sulfonatesodium salt assay (TNBS assay). Numerous additional references known tothose in the art provide suitable methods (See e.g., Wells et al.,Nucleic Acids Res. 11:7911-7925 [1983]; Christianson et al., Anal.Biochem., 223:119-129 [1994]; and Hsia et al., Anal Biochem.,242:221-227 [1999]).

Means for determining the levels of secretion of a protein of interestin a host cell and detecting expressed proteins include the use ofimmunoassays with either polyclonal or monoclonal antibodies specificfor the protein. Examples include enzyme-linked immunosorbent assay(ELISA), radioimmunoassay (RIA), fluorescence immunoassay (FIA), andfluorescent activated cell sorting (FACS). However, other methods areknown to those in the art and find use in assessing the protein ofinterest (See e.g., Hampton et al., Serological Methods, A LaboratoryManual, APS Press, St. Paul, Minn. [1990]; and Maddox et al., J. Exp.Med., 158:1211 [1983]). In some preferred embodiments, secretion of aprotein of interest is higher in the altered strain obtained using thepresent invention than in a corresponding unaltered host. As known inthe art, the altered Bacillus cells produced using the present inventionare maintained and grown under conditions suitable for the expressionand recovery of a polypeptide of interest from cell culture (See e.g.,Hardwood and Cutting (eds.) Molecular Biological Methods for Bacillus.John Wiley & Sons [1990]).

B. Large Chromosomal Deletions

As indicated above, in addition to single and multiple gene deletions,the present invention provides large chromosomal deletions. In somepreferred embodiments of the present invention, an indigenouschromosomal region or fragment thereof is deleted from a Bacillus hostcell to produce an altered Bacillus strain. In some embodiments, theindigenous chromosomal region includes prophage regions, antimicrobialregions, (e.g., antibiotic regions), regulator regions, multi-contiguoussingle gene regions and/or operon regions. The coordinates delineatingindigenous chromosomal regions referred to herein are specifiedaccording to the Bacillus subtilis strain 168 chromosome map. Numbersgenerally relate to the beginning of the ribosomal binding site, ifpresent, or the end of the coding region, and generally do not include aterminator that might be present. The Bacillus subtilis genome of strain168 is well known (See, Kunst et al., Nature 390:249-256 [1997]; andHenner et al., Microbiol. Rev., 44:57-82 [1980]), and is comprised ofone 4215 kb chromosome. However, the present invention also includesanalogous sequences from any Bacillus strain. Particularly preferred areother B. subtilis strains, B. licheniformis strains and B.amyloliquefaciens strains.

In some embodiments, the indigenous chromosomal region includes prophagesegments and fragments thereof. A “prophage segment” is viral DNA thathas been inserted into the bacterial chromosome wherein the viral DNA iseffectively indistinguishable from normal bacterial genes. The B.subtilis genome is comprised of numerous prophage segments; thesesegments are not infective. (Seaman et al., Biochem., 3:607-613 [1964];and Stickler et al., Virol., 26:142-145 [1965]). Although any one of theBacillus subtilis prophage regions may be deleted, reference is made tothe following non-limiting examples.

One prophage region that is deleted in some embodiments of the presentinvention is a sigma K intervening “skin” element. This region is foundat about 2652600 bp (spoIVCA) to 2700579 bp (yqaB) of the B. subtilis168 chromosome. Using the present invention, about a 46 kb segment wasdeleted, corresponding to 2653562 bp to 2699604 bp of the chromosome.This element is believed to be a remnant of an ancestral temperate phagewhich is position within the SIGK ORF, between the genes spoIVCB andspoIIIC. However, it is not intended that the present invention belimited to any particular mechanism or mode of action involving thedeleted region. The element has been shown to contain 57 open readingframes with putative ribosome binding sites (See, Takemaru et al.,Microbiol., 141:323-327 [1995]). During spore formation in the mothercell, the skin element is excised leading to the reconstruction of thesigK gene.

Another region suitable for deletion is a prophage 7 region. This regionis found at about 2701208 bp (yrkS) to 2749572 bp (yraK) of the B.subtilis 168 chromosome. Using the present invention, about a 48.5 kbsegment was deleted, corresponding to 2701087 bp to 2749642 bp of thechromosome.

A further region is a skin+prophage 7 region. This region is found atabout 2652151 bp to 2749642 bp of the B. subtilis 168 chromosome. Usingthe present invention, a segment of about 97.5 kb was deleted. Thisregion also includes the intervening spoIIIC gene. The skin/prophage 7region includes but is not limited to the following genes: spoIVCA-DNArecombinase, blt (multidrug resistance), cypA (cytochrome P450-likeenzyme), czcD (cation-efflux system membrane protein), and rapE(response regulator aspartate phosphatase).

Yet another region is the PBSX region. This region is found at about1319884 bp (xkdA) to 1347491 bp (xlyA) of the B. subtilis 168chromosome. Using the present invention, a segment of about 29 kb wasdeleted, corresponding to 1319663 to 1348691 bp is of the chromosome.Under normal non-induced conditions this prophage element isnon-infective and is not bactericidal (except for a few sensitivestrains such as W23 and S31). It is inducible with mitomycin C andactivated by the SOS response and results in cell lysis with the releaseof phage-like particles. The phage particles contain bacterialchromosomal DNA and kill sensitive bacteria without injecting DNA.(Canosi et al., J. Gen. Virol. 39: 81-90 [1978]). This region includesthe following non-limiting list of genes: xtmA-B; xkdA-K and M-X, xre,xtrA, xpf, xep, xhlA-B and xlyA.

A further region is the SPβ region. This region is found at about2150824 bp (yodU) to 2286246 bp (ypqP) of the B. subtilis 168chromosome. Using the present invention, a segment of about 133.5 kb wasdeleted, corresponding to 2151827 to 2285246 bp of the chromosome. Thiselement is a temperate prophage whose function has not yet beencharacterized. However, genes in this region include putative spore coatproteins (yodU, sspC, yokH), putative stress response proteins (yorD,yppQ, ypnP) and other genes that have homology to genes in the sporecoat protein and stress response genes such as members of the yomoperon. Other genes is this region include: yot; yos, yoq, yop, yon,yom, yoz, yol, yok, ypo, and ypm.

An additional region is the prophage 1 region. This region is found atabout 202098 bp (ybbU) to 220015 bp (ybdE) of the B. subtilis 168chromosome. Using the present invention, a segment of about 18.0 kb wasdeleted, corresponding to 202112 to 220141 bp of the chromosome. Genesin this region include the AdaA/B operon which provides an adaptiveresponse to DNA alkylation and ndhF which codes for NADH dehydrogenase,subunit 5.

A further region is the prophage 2 region. This region is found at about529069 bp (ydcL) to 569493 bp (ydeJ) of the B. subtilis 168 chromosome.Using the present invention, a segment of about 40.5 kb was deleted,corresponding to 529067 to 569578 bp of the chromosome. Genes in thisregion include rapI/phrI (response regulator asparate phosphatase), sacV(transcriptional regulator of the levansucrase) and cspC.

Another region is the prophage 3 region. Using the present invention, asegment of about 50.7 kb segment was deleted, corresponding to about652000 to 664300 bp of the B. subtilis 168 chromosome.

Yet another region is the prophage 4 region. This region is found atabout 1263017 bp (yjcM) to 1313627 bp (yjoA) of the B. subtilis 168chromosome. Using the present invention, a segment of about 2.3 kb wasdeleted, corresponding to 1262987 to 1313692 bp of the chromosome.

An additional region is the prophage 5 region. Using the presentinvention a segment of about 20.8 kb segment was deleted, correspondingto about 1879200 to 1900000 bp of the B. subtilis 168 chromosome.

Another region is the prophage 6 region. Using the present invention asegment of about a 31.9 kb segment was deleted, corresponding to about2046050 to 2078000 bp in the B. subtilis 168 chromosome.

In further embodiments, the indigenous chromosomal region includes oneor more operon regions, multi-contiguous single gene regions, and/oranti-microbial regions. In some embodiments, these regions include thefollowing:

1) The PPS Operon Region:

This region is found at about 1959410 bp (ppsE) to 1997178 bp (ppsA) ofthe Bacillus subtilis 168 chromosome. Using the present invention, asegment of about 38.6 kb was deleted, corresponding to about 1960409 to1998026 bp of the chromosome. This operon region is involved inantimicrobial synthesis and encodes plipastatin synthetase;

2) The PKS Operon Region:

This region is found at about 1781110 bp (pksA) to 1857712 bp (pksR) ofthe B. subtilis 168 chromosome. Using the present invention, a segmentof about 76.2 kb was deleted, corresponding to about 1781795 to 1857985bp of the chromosome. This region encodes polyketide synthase and isinvolved in anti-microbial synthesis. (Scotti et al., Gene, 130:65-71[1993]);

3) The yvfF-yveK Operon Region:

This region is found at about 3513149 bp (yvfF) to 3528184 bp (yveK) ofthe B. subtilis 168 chromosome. Using the present invention, a segmentof about 15.8 kb was deleted, corresponding to about 3513137 to 3528896bp of the chromosome. This region codes for a putative polysaccharide(See, Dartois et al., Seventh International Conference on Bacillus(1993) Institute Pasteur [1993], page 56). This region includes thefollowing genes; yvfA-F, yveK-T and sir. The slr gene region which isfound at about 3529014-3529603 bp of the B. subtilis 168 chromosomeencompasses about a 589 bp segment. This region is the regulator regionof the yvfF-yveK operon;

4) The DHB Operon Region:

This region is found at about 3279750 bp (yukL) to 3293206 bp (yuiH) ofthe B. subtilis 168 chromosome. Using the present invention, a segmentof about 13.0 kb was deleted, corresponding to 3279418-3292920 bp of thechromosome. This region encodes the biosynthetic template for thecatecholic siderophone 2,3-dihydroxy benzoate-glycine-threonine trimericester bacilibactin. (See, May et al., J. Biol. Chem., 276:7209-7217[2001]). This region includes the following genes: yukL, yukM, dhbA-C, Eand F, and yuiI-H.

While the regions, as described above, are examples of preferredindigenous chromosomal regions to be deleted, in some embodiments of thepresent invention, a fragment of the region is also deleted. In someembodiments, such fragments include a range of about 1% to 99% of theindigenous chromosomal region. In other embodiments, fragments include arange of about 5% to 95% of the indigenous chromosomal region. In yetadditional embodiments, fragments comprise at least 99%, 98%, 97%, 96%,95%, 94%, 93%, 92%, 90%, 88%, 85%, 80%, 75%, 70%, 65%, 50%, 40%, 30%,25%, 20% and 10% of the indigenous chromosomal region.

Further non-limiting examples of fragments of indigenous chromosomalregions to be deleted with reference to the chromosomal location in theB. subtilis 168 chromosome include the following:

a) for the skin region:

-   -   i) a coordinate location of about 2666663 to 2693807, which        includes yqcC to yqaM, and    -   ii) a coordinate location of about 2658440 to 2659688, which        includes rapE to phrE;

b) for the PBSX prophage region:

-   -   i) a coordinate location of about 1320043 to 1345263, which        includes xkdA to xkdX, and    -   ii) a coordinate location of about 1326662 to 1345102, which        includes xkdE to xkdW;

c) for the SPβ region:

-   -   i) a coordinate location of about 2149354 to 2237029, which        includes yodV to yonA;

d) for the DHB region:

-   -   i) a coordinate location of about 3282879 to 3291353, which        includes dhbF to dhbA;

e) for the yvfF-yveK region:

-   -   i) a coordinate location of about 3516549 to 3522333, which        includes yvfB to yveQ,    -   ii) a coordinate location of about 3513181 to 3528915, which        includes yvfF to yveK, and    -   iii) a coordinate location of about 3521233 to 3528205, which        includes yveQ to yveL;

f) for the prophage 1 region:

-   -   i) a coordinate location of about 213926 to 220015, which        includes ybcO to ybdE, and    -   ii) a coordinate location of about 214146 to 220015, which        includes ybcP to ybdE;

g) for the prophage 2 region:

-   -   i) a coordinate location of about 546867 to 559005, which        includes rapI to cspC; and

h) for the prophage 4 region:

-   -   i) a coordinate location of about 1263017 to 675421, which        includes yjcM to ydjJ.

The number of fragments of indigenous chromosomal regions which aresuitable for deletion are numerous, because a fragment may be comprisedof only a few bps less than the identified indigenous chromosomalregion. Furthermore, many of the identified indigenous chromosomalregions encompass a large number of genes. Those of skill in the art arecapable of easily determining which fragments of the indigenouschromosomal regions are suitable for deletion for use in a particularapplication.

The definition of an indigenous chromosomal region is not so strict asto exclude a number of adjacent nucleotides to the defined segment. Forexample, while the SPβ region is defined herein as located atcoordinates 2150824 to 2286246 of the B. subtilis 168 chromosome, anindigenous chromosomal region may include a further 10 to 5000 bp, afurther 100 to 4000 bp, or a further 100 to 1000 bp on either side ofthe region. The number of bp on either side of the region is limited bythe presence of another gene not included in the indigenous chromosomalregion targeted for deletion.

As stated above, the location of specified regions herein disclosed arein reference to the B. subtilis 168 chromosome. Other analogous regionsfrom Bacillus strains are included in the definition of an indigenouschromosomal region. While the analogous region may be found in anyBacillus strain, particularly preferred analogous regions are regionsfound in other Bacillus subtilis strains, Bacillus licheniformis strainsand Bacillus amyloliquefaciens strains.

In certain embodiments, more than one indigenous chromosomal region orfragment thereof is deleted from a Bacillus strain. However, thedeletion of one or more indigenous chromosomal regions or fragmentsthereof does not deleteriously affect reproductive viability of thestrain which includes the deletion. In some embodiments, two indigenouschromosomal regions or fragments thereof are deleted. In additionalembodiments, three indigenous chromosomal regions or fragments thereofare deleted. In yet another embodiment, four indigenous chromosomalregions or fragments thereof are deleted. In a further embodiment, fiveindigenous chromosomal regions or fragments thereof are deleted. Inanother embodiment, as many as 14 indigenous chromosomal regions orfragments thereof are deleted. In some embodiments, the indigenouschromosomal regions or fragments thereof are contiguous, while in otherembodiments, they are located on separate regions of the Bacilluschromosome.

A strain of any member of the genus Bacillus comprising a deletedindigenous chromosomal region or fragment thereof finds use in thepresent invention. In some preferred embodiments, the Bacillus strain isselected from the group consisting of B. subtilis strains, B.amyloliquefaciens strains, B. lentus strains, and B. licheniformisstrains.

In some preferred embodiments, the strain is an industrial Bacillusstrain, and most preferably an industrial B. subtilis strain. In afurther preferred embodiment, the altered Bacillus strain is aprotease-producing strain. In some particularly preferred embodiments,it is a B. subtilis strain that has been previously engineered toinclude a polynucleotide encoding a protease enzyme.

As indicated above, a Bacillus strain in which an indigenous chromosomalregion or fragment thereof has been deleted is referred to herein as “analtered Bacillus strain.” In preferred embodiments of the presentinvention, the altered Bacillus strain has an enhanced level ofexpression of a protein of interest (i.e., the expression of the proteinof interest is enhanced, compared to a corresponding unaltered Bacillusstrain grown under the same growth conditions).

One measure of enhancement is the secretion of the protein of interest.In some embodiments, production of the protein of interest is enhancedby at least 0.5%, 1.0%, 1.5%, 2.0%, 2.5%, 3.0%, 4.0%, 5.0%, 8.0%, 10%,15%, 20% and 25% or more, compared to the corresponding unalteredBacillus strain. In other embodiments, production of the protein ofinterest is enhanced by between about 0.25% to 20%; 0.5% to 15% and 1.0%to 10%, compared to the corresponding unaltered Bacillus strain asmeasured in grams of protein produced per liter.

The altered Bacillus strains provided by the present inventioncomprising a deletion of an indigenous chromosomal region or fragmentthereof are produced using any suitable methods, including but notlimited to the following means. In one general embodiment, a DNAconstruct is introduced into a Bacillus host. The DNA constructcomprises an inactivating chromosomal segment, and in some embodiments,further comprises a selective marker. Preferably, the selective markeris flanked on both the 5′ and 3′ ends by one section of the inactivatingchromosomal segment.

In some embodiments, the inactivating chromosomal segment, whilepreferably having 100% sequence identity to the immediate upstream anddownstream nucleotides of an indigenous chromosomal region to be deleted(or a fragment of said region), has between about 70 to 100%, about 80to 100%, about 90 to 100%, and about 95 to 100% sequence identity to theupstream and downstream nucleotides of the indigenous chromosomalregion. Each section of the inactivating chromosomal segment mustinclude sufficient 5′ and 3′ flanking sequences of the indigenouschromosomal region to provide for homologous recombination with theindigenous chromosomal region in the unaltered host.

In some embodiments, each section of the inactivating chromosomalsegment comprises about 50 to 10,000 base pairs (bp). However, lower orhigher bp sections find use in the present invention. Preferably, eachsection is about 50 to 5000 bp, about 100 to 5000 bp, about 100 to 3000bp; 100 to 2000 bp; about 100 to 1000 bp; about 200 to 4000 bp, about400 to 3000 bp, about 500 to 2000 bp, and also about 800 to 1500 bp.

In some embodiments, a DNA construct comprising a selective marker andan inactivating chromosomal segment is assembled in vitro, followed bydirect cloning of said construct into a competent Bacillus host, suchthat the DNA construct becomes integrated into the Bacillus chromosome.For example, PCR fusion and/or ligation are suitable for assembling aDNA construct in vitro. In some embodiments, the DNA construct is anon-plasmid construct, while in other embodiments, it is incorporatedinto a vector (i.e., a plasmid). In some embodiments, a circular plasmidis used, and the circular plasmid is cut using an appropriaterestriction enzyme (i.e., one that does not disrupt the DNA construct).Thus, linear plasmids find use in the present invention (See e.g., FIG.1; and Perego, “Integrational Vectors for Genetic Manipulation inBacillus subtilis,” in Bacillus subtilis and other Gram-PositiveBacteria, Sonenshein. et al., Eds., Am. Soc. Microbiol., Washington,D.C. [1993]).

In some embodiments, a DNA construct or vector, preferably a plasmidincluding an inactivating chromosomal segment includes a sufficientamount of the 5′ and 3′ flanking sequences (seq) of the indigenouschromosomal segment or fragment thereof to provide for homologousrecombination with the indigenous chromosomal region or fragment thereofin the unaltered host. In another embodiment, the DNA construct includesrestriction sites engineered at upstream and downstream ends of theconstruct. Non-limiting examples of DNA constructs useful according tothe invention and identified according to the coordinate locationinclude:

1. A DNA construct for deleting a PBSX region: [5′ flanking seq1318874-1319860 bp which includes the end of yjqB and the entire yjpCincluding the ribosome binding site (RBS)]—marker gene—[3′ flankingseq1348691-1349656 bp which includes a terminator and upstream sectionof the pit].

2. A DNA construct for deleting a prophage 1 region: [5′ flanking seq201248-202112 bp which contains the entire glmS including the RBS andterminator and the ybbU RBS]—marker gene—[3′ flanking seq 220141-221195bp which includes the entire ybgd including the RBS].

3. A DNA construct for deleting a prophage 2 region: [5′ flanking seq527925-529067 bp which contains the end of ydcK, the entire tRNAs asfollows: trnS-Asn, trnS-Ser, trnS-Glu, trnS-Gln, trnS-Lys, trnS-Leu1 andtrnS-leu2]—marker gene—[3′ flanking seq 569578-571062 bp which containsthe entire ydeK and upstream part of ydeL].

4. A DNA construct for deleting a prophage 4 region: [5′ flanking seq1263127-1264270 bp which includes part of yjcM]—marker gene—[3′ flankingseq 1313660-1314583 bp which contains part of yjoB including the RBS].

5. A DNA construct for deleting a yvfF-yveK region: [5′ flanking seq3512061-3513161 bp which includes part of sigL, the entire yvfG and thestart of yvfF]—marker gene—[3′ flanking seq 3528896-3529810 bp whichincludes the entire slr and the start of pnbA.

6. A DNA construct for deleting a DHB operon region: [5′ flanking seq3278457-3280255 which includes the end of ald including the terminator,the entire yuxI including the RBS, the entire yukJ including the RBS andterminator and the end of yukL]—marker gene—[3′ flanking seq3292919-3294076 which includes the end of yuiH including the RBS, theentire yuiG including the RBS and terminator and the upstream end ofyuiF including the terminator.

Whether the DNA construct is incorporated into a vector or used withoutthe presence of plasmid DNA, it is introduced into a microorganism,preferably an E. coli cell or a competent Bacillus cell.

Methods for introducing DNA into Bacillus cells involving plasmidconstructs and transformation of plasmids into E. coli are well known.The plasmids are subsequently isolated from E. coli and transformed intoBacillus. However, it is not essential to use intervening microorganismssuch as E. coli, and in some embodiments, a DNA construct or vector isdirectly introduced into a Bacillus host.

In a preferred embodiment, the host cell is a Bacillus sp. (See e.g.,U.S. Pat. No. 5,264,366, U.S. Pat. No. 4,760,025, and RE 34,6060). Insome embodiments, the Bacillus strain of interest is an alkalophilicBacillus. Numerous alkalophilic Bacillus strains are known (See e.g.,U.S. Pat. No. 5,217,878; and Aunstrup et al., Proc IV IFS: Ferment.Tech. Today, 299-305 [1972]). Another type of Bacillus strain ofparticular interest is a cell of an industrial Bacillus strain. Examplesof industrial Bacillus strains include, but are not limited to B.licheniformis, B. lentus, B. subtilis, and B. amyloliquefaciens. Inadditional embodiments, the Bacillus host strain is selected from thegroup consisting of B. licheniformis, B subtilis, B. lentus, B. brevis,B. stearothermophilus, B. alkalophilus, B. amyloliquefaciens, B.coagulans, B. circulans, B. pumilus, B. thuringiensis, B. clausii, andB. megaterium. In particularly preferred embodiments, B. subtilis cellsare used.

In some embodiments, the industrial host strains are selected from thegroup consisting of non-recombinant strains of Bacillus sp., mutants ofa naturally-occurring Bacillus strain, and recombinant Bacillus hoststrains. Preferably, the host strain is a recombinant host strain,wherein a polynucleotide encoding a polypeptide of interest has beenpreviously introduced into the host. A further preferred host strain isa Bacillus subtilis host strain, and particularly a recombinant Bacillussubtilis host strain. Numerous B. subtilis strains are known andsuitable for use in the present invention (See e.g., 1A6 (ATCC 39085),168 (1A01), SB19, W23, Ts85, B637, PB1753 through PB1758, PB3360, JH642,1A243 (ATCC 39,087), ATCC 21332, ATCC 6051, MI113, DE100 (ATCC 39,094),GX4931, PBT 110, and PEP 211strain; Hoch et al., Genetics, 73:215-228[1973]; U.S. Pat. No. 4,450,235; U.S. Pat. No. 4,302,544; EP 0134048;Palva et al., Gene, 19:81-87 [1982]; Fahnestock and Fischer, J.Bacteriol., (1986) 165:796-804 [1986]; and Wang et al, Gene 69:39-47[1988]). Of particular interest as expression hosts are industrialprotease-producing Bacillus strains. By using these strains, the highefficiency seen for production of the protease is further enhanced bythe altered Bacillus strain of the present invention.

Industrial protease producing Bacillus strains provide particularlypreferred expression hosts. In some preferred embodiments, use of thesestrains in the present invention provides further enhancements inefficiency and protease production. As indicated above, there are twogeneral types of proteases are typically secreted by Bacillus sp.,namely neutral (or “metalloproteases”) and alkaline (or “serine”)proteases. Also as indicated above, subtilisin is a preferred serineprotease for use in the present invention. A wide variety of Bacillussubtilisins have been identified and sequenced, for example, subtilisin168, subtilisin BPN′, subtilisin Carlsberg, subtilisin DY, subtilisin147 and subtilisin 309 (See e.g., EP 414279 B; WO 89/06279; and Stahl etal., J. Bacteriol., 159:811-818 [1984]). In some embodiments of thepresent invention, the Bacillus host strains produce mutant (e.g.,variant) proteases. Numerous references provide examples of variantproteases and reference (See e.g., WO 99/20770; WO 99/20726; WO99/20769; WO 89/06279; RE 34,606; U.S. Pat. No. 4,914,031; U.S. Pat. No.4,980,288; U.S. Pat. No. 5,208,158; U.S. Pat. No. 5,310,675; U.S. Pat.No. 5,336,611; U.S. Pat. No. 5,399,283; U.S. Pat. No. 5,441,882; U.S.Pat. No. 5,482,849; U.S. Pat. No. 5,631,217; U.S. Pat. No. 5,665,587;U.S. Pat. No. 5,700,676; U.S. Pat. No. 5,741,694; U.S. Pat. No.5,858,757; U.S. Pat. No. 5,880,080; U.S. Pat. No. 6,197,567; and U.S.Pat. No. 6,218,165.

In yet another embodiment, a preferred Bacillus host is a Bacillus sp.that includes a mutation or deletion in at least one of the followinggenes, degU, degS, degR and degQ. Preferably the mutation is in a degUgene, and more preferably the mutation is degU(Hy)32. (See, Msadek etal., J. Bacteriol., 172:824-834 [1990]; and Olmos et al., Mol. Gen.Genet., 253:562-567 [1997]). A most preferred host strain is a Bacillussubtilis carrying a degU32(Hy) mutation. In a further embodiment, theBacillus host comprises a mutation or deletion in scoC4, (See, Caldwellet al., J. Bacteriol., 183:7329-7340 [2001]); spoIIE (See, Arigoni etal., Mol. Microbiol., 31:1407-1415 [1999]); oppA or other genes of theopp operon (See, Perego et al., Mol. Microbiol., 5:173-185 [1991]).Indeed, it is contemplated that any mutation in the opp operon thatcauses the same phenotype as a mutation in the oppA gene will find usein some embodiments of the altered Bacillus strain of the presentinvention. In some embodiments, these mutations occur alone, while inother embodiments, combinations of mutations are present. In someembodiments, an altered Bacillus of the invention is obtained from aBacillus host strain that already includes a mutation in one or more ofthe above-mentioned genes. In alternate embodiments, an altered Bacillusof the invention is further engineered to include mutation in one ormore of the above-mentioned genes.

In some embodiments, two or more DNA constructs are introduced into aBacillus host cell, resulting in the deletion of two or more indigenouschromosomal regions in an altered Bacillus. In some embodiments, theseregions are contiguous, (e.g., the skin plus prophage 7 region), whilein other embodiments, the regions are separated (e.g., the PBSX regionand the PKS region; the skin region and the DHB region; or the PKSregion, the SPβ region and the yvfF-yveK region).

Those of skill in the art are well aware of suitable methods forintroducing polynucleotide sequences into bacterial (e.g., E. coli andBacillus) cells (See e.g., Ferrari et al., “Genetics,” in Harwood et al.(ed.), Bacillus, Plenum Publishing Corp. [1989], pages 57-72; See also,Saunders et al., J. Bacteriol., 157:718-726 [1984]; Hoch et al., J.Bacteriol., 93:1925-1937 [1967]; Mann et al., Current Microbiol.,13:131-135 [1986]; and Holubova, Folia Microbiol., 30:97 [1985]; for B.subtilis, Chang et al., Mol. Gen. Genet., 168:11-115 [1979]; for B.megaterium, Vorobjeva et al., FEMS Microbiol. Lett., 7:261-263 [1980];for B amyloliquefaciens, Smith et al., Appl. Env. Microbiol., 51:634(1986); for B. thuringiensis, Fisher et al., Arch. Microbiol.,139:213-217 [1981]; and for B. sphaericus, McDonald, J. Gen. Microbiol.,130:203 [1984]). Indeed, such methods as transformation includingprotoplast transformation and congression, transduction, and protoplastfusion are known and suited for use in the present invention. Methods oftransformation are particularly preferred to introduce a DNA constructprovided by the present invention into a host cell.

In addition to commonly used methods, in some embodiments, host cellsare directly transformed (i.e., an intermediate cell is not used toamplify, or otherwise process, the DNA construct prior to introductioninto the host cell). Introduction of the DNA construct into the hostcell includes those physical and chemical methods known in the art tointroduce DNA into a host cell, without insertion into a plasmid orvector. Such methods include but are not limited to calcium chlorideprecipitation, electroporation, naked DNA, liposomes and the like. Inadditional embodiments, DNA constructs are co-transformed with a plasmidwithout being inserted into the plasmid. In a further embodiments, aselective marker is deleted or substantially excised from the alteredBacillus strain by methods known in the art (See, Stahl et al., J.Bacteriol., 158:411-418 [1984]; and the conservative site-specificrecombination [CSSR] method of Palmeros et al., described in Palmeros etal., Gene 247:255-264 [2000]). In some preferred embodiments, resolutionof the vector from a host chromosome leaves the flanking regions in thechromosome while removing the indigenous chromosomal region.

In some embodiments, host cells are transformed with one or more DNAconstructs according to the present invention to produce an alteredBacillus strain wherein is two or more genes have been inactivated inthe host cell. In some embodiments, two or more genes are deleted fromthe host cell chromosome. In alternative embodiments, two or more genesare inactivated by insertion of a DNA construct. In some embodiments,the inactivated genes are contiguous (whether inactivated by deletionand/or insertion), while in other embodiments, they are not contiguousgenes.

As indicated above, there are various assays known to those of ordinaryskill in the art for detecting and measuring activity of intracellularlyand extracellularly expressed polypeptides. In particular, forproteases, there are assays based on the release of acid-solublepeptides from casein or hemoglobin measured as absorbance at 280 nm orcolorimetrically using the Folin method (See e.g., Bergmeyer et al.,“Methods of Enzymatic Analysis” vol. 5, Peptidases, Proteinases andtheir Inhibitors, Verlag Chemie, Weinheim [1984]). Other assays involvethe solubilization of chromogenic substrates (See e.g., Ward,“Proteinases,” in Fogarty (ed.)., Microbial Enzymes and Biotechnology,Applied Science, London, [1983], pp 251-317). Other exemplary assaysinclude succinyl-Ala-Ala-Pro-Phe-para nitroanilide assay (SAAPFpNA) andthe 2,4,6-trinitrobenzene sulfonate sodium salt assay (TNBS assay).Numerous additional references known to those in the art providesuitable methods (See e.g., Wells et al., Nucleic Acids Res.11:7911-7925 [1983]; Christianson et al., Anal. Biochem., 223:119-129[1994]; and Hsia et al., Anal Biochem., 242:221-227 [1999]).

Also as indicated above, means for determining the levels of secretionof a protein of interest in a host cell and detecting expressed proteinsinclude the use of immunoassays with either polyclonal or monoclonalantibodies specific for the protein. Examples include enzyme-linkedimmunosorbent assay (ELISA), radioimmunoassay (RIA), fluorescenceimmunoassay (FIA), and fluorescent activated cell sorting (FACS).However, other methods are known to those in the art and find use inassessing the protein of interest (See e.g., Hampton et al., SerologicalMethods, A Laboratory Manual, APS Press, St. Paul, Minn. [1990]; andMaddox et al., J. Exp. Med., 158:1211 [1983]). In some preferredembodiments, secretion of a protein of interest is higher in the alteredstrain obtained using the present invention than in a correspondingunaltered host. As known in the art, the altered Bacillus cells producedusing the present invention are maintained and grown under conditionssuitable for the expression and recovery of a polypeptide of interestfrom cell culture (See e.g., Hardwood and Cutting (eds.) MolecularBiological Methods for Bacillus, John Wiley & Sons [1990]).

The manner and method of carrying out the present invention may be morefully understood by those of skill in the art by reference to thefollowing examples, which examples are not intended in any manner tolimit the scope of the present invention or of the claims directedthereto.

EXPERIMENTAL

The following Examples are provided in order to demonstrate and furtherillustrate certain preferred embodiments and aspects of the presentinvention and are not to be construed as limiting the scope thereof.

In the experimental disclosure which follows, the followingabbreviations apply: ° C. (degrees Centigrade); rpm (revolutions perminute); H₂O (water); dH₂O (deionized water); (HCl (hydrochloric acid);aa (amino acid); bp (base pair); kb (kilobase pair); kD (kilodaltons);gm (grams); μg (micrograms); mg (milligrams); ng (nanograms); μl(microliters); ml (milliliters); mm (millimeters); nm (nanometers); μm(micrometer); M (molar); mM (millimolar); μM (micromolar); U (units); V(volts); MW (molecular weight); sec (seconds); min(s) (minute/minutes);hr(s) (hour/hours); MgCl₂ (magnesium chloride); NaCl (sodium chloride);OD₂₈₀ (optical density at 280 nm); OD₆₀₀ (optical density at 600 nm);PAGE (polyacrylamide gel electrophoresis); PBS (phosphate bufferedsaline [150 mM NaCl, 10 mM sodium phosphate buffer, pH 7.2]); PEG(polyethylene glycol); PCR (polymerase chain reaction); RT-PCR (reversetranscription PCR); SDS (sodium dodecyl sulfate); Tris(tris(hydroxymethyl)aminomethane); w/v (weight to volume); v/v (volumeto volume); LA medium (per liter: Difco Tryptone Peptone 20 g, DifcoYeast Extract 10 g, EM Science NaCl 1 g, EM Science Agar 17.5 g, dH20 to1 L); ATCC (American Type Culture Collection, Rockville, Md.); Clontech(CLONTECH Laboratories, Palo Alto, Calif.); Difco (Difco Laboratories,Detroit, Mich.); GIBCO BRL or Gibco BRL (Life Technologies, Inc.,Gaithersburg, Md.); Invitrogen (Invitrogen Corp., San Diego, Calif.);NEB (New England Biolabs, Beverly, Mass.); Sigma (Sigma Chemical Co.,St. Louis, Mo.); Takara (Takara Bio Inc. Otsu, Japan); Roche Diagnosticsand Roche (Roche Diagnostics, a division of F. Hoffmann La Roche, Ltd.,Basel, Switzerland); EM Science (EM Science, Gibbstown, N.J.); Qiagen(Qiagen, Inc., Valencia, Calif.); Stratagene (Stratagene CloningSystems, La Jolla, Calif.); Affymetrix (Affymetrix, Santa Clara,Calif.).

Example 1 Creation of Deletion Strains

This Example describes “Method 1,” which is also depicted in FIG. 1. Inthis method, E. coli was used to produce a pJM102 plasmid vectorcarrying the DNA construct to be transformed into Bacillus strains.(See, Perego, supra). Regions immediately flanking the 5′ and 3′ ends ofthe deletion site were PCR amplified. PCR primers were designed to beapproximately 37 base pairs in length, including 31 base pairshomologous to the Bacillus subtilis chromosome and a 6 base pairrestriction enzyme site located 6 base pairs from the 5′ end of theprimer. Primers were designed to engineer unique restriction sites atthe upstream and downstream ends of the construct and a BamHI sitebetween the two fragments for use in cloning. Primers for theantimicrobial markers contained BamHI sites at both ends of thefragment. Where possible, PCR primers were designed to remove promotersof deleted indigenous chromosomal regions, but to leave all terminatorsin the immediate area. The primary source of chromosome sequence, genelocalization, and promoter and terminator information was obtained fromKunst et al., (1997) supra and also obtainable from the SubtiList WorldWide Web Server known to those in the art (See e.g., Moszer et al.,supra). Numerous deletions have been made using the present invention. Alist of primer sequences from deletions created by this method isprovided in Table 1. Reference is also made to FIG. 2 for an explanationof the primer naming system. TABLE 1 Primers Restriction Enzyme PrimerEngineered SEQ ID Name Into Primer Primer Sequence NO PBSX-UF XbaICTACATTCTAGACGATTTGTTTGATCGATATGTGGAAGC 60 PBSX-UR BamHIGGCTGAGGATCCATTCCTCAGCCCAGAAGAGAACCTA 61 PBSX-DF BamHITCCCTCGGATCCGAAATAGGTTCTGCTTATTGTATTCG 62 PBSX-DR SacIAGCGTTGAGCTCGCGCCATGCCATTATAUGGCTGCTG 63 Pphage 1- EcoRIGTGACGGAATTCCACGTGCGTCTTATATTGCTGAGCTT 64 Pphage 1- BamHICGTTTTGGATCCAAAAACACCCCTTTAGATAATCTTAT 65 Pphage 1- BamHIATCAAAGGATCCGCTATGCTCCAAATGTACACCTTTCCGT 66 Pphage 1- PstIATATTTCTGCAGGCTGATATAAATAATACTGTGTGTTCC 67 Pphage 2- SacICATCTTGAATTCAAAGGGTACAAGCACAGAGACAGAG 68 Pphage 2- BamHITGACTTGGATCCGGTAAGTGGGCAGTTTGTGGGCAGT 69 Pphage 2- BamHITAGATAGGATCCTATTGAAAACTGTTTAAGAAGAGGA 70 Pphage 2- PstICTGATTCTGCAGGAGTGTTTTTGAAGGAAGCTTCATT 71 Pphage 4- KpnICTCCGCGGTACCGTCACGAATGCGCCTCTTATTCTAT 72 Pphage 4- BamHITCGCTGGGATCCUGGCGCCGTGGAATCGATTTTGTCC 73 Pphage 4- BamHIGCAATGGGATCCTATATCAACGGTTATGAATTCACAA 74 Pphage 4- PstICCAGAACTGCAGGAGCGAGGCGTCTCGCTGCCTGAAA 75 PPS-UF SacIGACAAGGAGCTCATGAAAAAAAGCATAAAGCTTTATGTTGC 76 PPS-UR BamHlGACAAGGGATCCCGGCATGTCCGTTATTACTTAATTTC 77 PPS-DF BamHIGACAAGGGATCCTGCCGCTTACCGGAAACGGA 78 PPS-DR XbaIGACAAGTCTAGATTATCGTTTGTGCAGTATTACTTG 79 SPβ-UF SacIACTGATGAGCTCTGCCTAAACAGCAAACAGCAGAAC 80 SPβ-UR BamHIACGAATGGATCCATCATAAAGCCGCAGCAGATTAAATAT 81 SPβ-DF BamHIACTGATGGATCCATCTTCGATAAATATGAAAGTGGC 82 SPβ-DR XbaIACTGATTCTAGAGCCTTTTTCTCTTGATGCAATTCTTC 83 PKS-UF XbaIGAGCCTCTAGAGCCCATTGAATCATTTGTTT 84 PKS-UR BamHIGAGCCGGATCCTTAAGGATGTCGTTTTTGTGTCT 85 PKS-DF BamHIGAGCCGGATCCATTTCGGGGTTCTCAAAAAAA 86 PKS-DR SacIGAGCCGAGCTCATGCAAATGGAAAAATTGAT 87 Skin-UF XbaIGAAGTTCTAGAGATTGTAATTACAAAAGGGGGGTG 88 Skin-UR BamHIGAAGTGGATCCTTTCACCGATCATAAAAGCCC 89 Skin-DE BamHITGAAAGGATCCATTTTTCATTGATTGTTAAGTC 90 Skin-DR SacIGAAGTTAGAGCTCGGGGGGGCATAAATTTCCCG 91 Phleo-UF BamHIGCTTATGGATCCGATACAAGAGAGGTCTCTCG 92 Phleo-DR BamHIGCTTATGGATCCCTGTCATGGCGCATTAACG 93 Spec-UF BamHIACTGATGGATCCATCGATTTTCGTTCGTGAATACATG 94 Spec-DR BamHIACTGATGGATCCCATATGCAAGGGTTTATTGTTTTC 95 CssS-UF XbaIGCACGTTCTAGACCACCGTCCCCTGTGTTGTATCCAC 96 CssS-UR BamHIAGGAAGGGATCCAGAGCGAGGAAGATGTAGGATGATC 97 CssS-DF BamHITGACAAGGATCCTGTATCATACCGCATAGCAGTGCC 98 CssS-DR SacITTCCGCGAGCTCGGCGAGAGCTTCAGACTCCGTCAGA 99 SBO- XbaIGAGCCTCTAGATCAGCGATTTGACGCGGCGC 100 SBO- BamHITTATCTGGATCCCTGATGAGCAATGATGGTAAGATAGA 101 SBO- BamHI GGGTAA GGATCCCCCAAAAGGGCATAGTCATTCTACT 102 SBO- Asp718 GAGATCGGTACCGTTTTGGGCCATATCGTGGATTTC 103 PhrC-UF HindIII GAGCC AAGCTTCATTGACAGCAACCAGGCAGATCTC 104 PhrC-DF PstIGCTTATAAGCTTGATACAAGAGAGGTCTCTCG 105 PhrC-UR PstIGCTTATAAGCTTCTGTCATGGCGCATTAACG 106 PhrC-DR SacI GAGCCGAGCTCCATGCCGATGAAGTCATCGTCGAGC 107 PhrC-UF- HindIII CGTGAA AAGCTTTCGCGGGATGTATGAATTTGATAAG 108 PhrC-DR- SacI TGTAGGGAGCTCGATGCGCCACAATGTCGGTACAACG 109The restriction sites are designated as follows: XbaI is TCTAGA; BamHIis GGATCC; SacI is GAGCTC; Asp718 is GGTACC; PstI is CTGCAG and HindIIIis AAGCTT. Also prophage is designated as “Pphage.”

In this method, 100 μL PCR reactions carried out in 150 μL Eppendorftubes containing 84 μL water, 10 μL PCR buffer, 1 μL of each primer(i.e., PKS-UF and PKS-UR), 2 μL of dNTPs, 1 μL of wild type Bacilluschromosomal DNA template, and 1 μL of polymerase. DNA polymerases usedincluded Taq Plus Precision polymerase and Herculase (Stratagene).Reactions were carried out in a Hybaid PCRExpress thermocycler using thefollowing program. The samples were first heated at 94° C. for 5minutes, then cooled to a 50° hold. Polymerase was added at this point.Twenty-five cycles of amplification consisted of 1 minute at 95° C., 1minute at 50° C. and 1 minute at 72° C. A final 10 minutes at 72° C.ensured complete elongation. Samples were held at is 4° C. for analysis.

After completion of the PCR, 10 μL of each reaction were run on anInvitrogen 1.2% agarose E-gel at 60 volts for 30 minutes to check forthe presence of a band at the correct size. All the gel electrophoresismethods described herein used these conditions. If a band was present,the remainder of the reaction tube was purified using the QiagenQiaquick® PCR purification kit according to the manufacturersinstructions, then cut with the appropriate restriction enzyme pair.Digests were performed at 37° C. for 1 hour as a 20 μL reactionconsisting of 9 μL of water, 2 μL of 10×BSA, 2 μL of an appropriate NEBrestriction buffer (according to the 2000-01 NEB Catalog and TechnicalReference), 5 μL of template, and 1 μL of each restriction enzyme. Forexample, the PBSX upstream fragment and CssS upstream fragments were cutwith XbaI and BamHI in NEB (New England BioLabs) restriction buffer B.The digested fragments were purified by gel electrophoresis andextraction using the Qiagen Qiaquick gel extraction kit following themanufacturer's instructions. FIGS. 5 and 6 provide gels showing theresults for various deletions.

Ligation of the fragments into a plasmid vector was done in two steps,using either the Takara ligation kit following the manufacturer'sinstructions or T4 DNA ligase (Reaction contents: 5 μL each insertfragment, 1 μL cut pJM102 plasmid, 3 μL T4 DNA ligase buffer, and 1 μLT4 DNA ligase). First, the cut upstream and downstream fragments wereligated overnight at 15° C. into unique restriction sites in the pJM102plasmid polylinker, connecting at the common BamHI site to re-form acircular plasmid. The pJM102 plasmid was cut with the unique restrictionenzyme sites appropriate for each deletion (See, Table 2; for cssS, XbaIand SacI were used) and purified as described above prior to ligation.This re-circularized plasmid was transformed into Invitrogen's “Top Ten”E. coli cells, using the manufacturers One Shot transformation protocol.

Transformants were selected on Luria-Bertani broth solidified with 1.5%agar (LA) plus 50 ppm carbanicillin containing X-gal for blue-whitescreening. Clones were picked and grown overnight at 37° C. in 5 mL ofLuria Bertani broth (LB) plus 50 ppm carbanicillin and plasmids wereisolated using Qiagen's Qiaquick Mini-Prep kit. Restriction analysisconfirmed the presence of the insert by cutting with the restrictionsites at each end of the insert to drop an approximately 2 kb band outof the plasmid. Confirmed plasmids with the insert were cut with BamHIto linearize them in digestion reactions as described above (with anadditional 1 μL of water in place of a second restriction enzyme),treated with 1 μL calf intestinal and shrimp phosphatases for 1 hour at37° C. to prevent re-circularization, and ligated to the antimicrobialresistance marker as listed in Table 2. Antimicrobial markers were cutwith BamHI and cleaned using the Qiagen Gel Extraction Kit followingmanufacturer's instructions prior to ligation. This plasmid was clonedinto E. coli as before, using 5 ppm phleomycin (phl) or 100 ppmspectinomycin (spc) as appropriate for selection. Confirmation of markerinsertion in isolated plasmids was done as described above byrestriction analysis with BamHI. Prior to transformation into B.subtilis, the plasmid was linearized with ScaI to ensure a doublecrossover event. TABLE 2 Unique Restriction Enzyme Pairs Used inDeletion Constructs Unique Restriction Deletion Name Enzyme PairAntimicrobial Marker Sbo XbaI-Asp718 spc Slr XbaI-SacI phleo YbcOXbaI-SacI spc Csn XbaI-SalI phleo PBSX XbaI-SacI phl PKS XbaI-SacI phlSPβ XbaI-SacI spec PPS XbaI-SacI spec Skin XbaI-SacI phl

Example 2 Creation of DNA Constructs Using PCR Fusion to Bypass E. coli

This Example describes “Method 2,” which is also depicted in FIG. 3.Upstream and downstream fragments were amplified as in Method 1, exceptthe primers were designed with 25 bp “tails” complementary to theantimicrobial marker's primer sequences. A “tail” is defined herein asbase pairs on the 5′ end of a primer that are not homologous to thesequence being directly amplified, but are complementary to anothersequence of DNA. Similarly, the primers for amplifying the antimicrobialcontain “tails” that are complementary to the fragments' primers. Forany given deletion, the DeletionX-UFfus and DeletionX-URfus are directcomplements of one another. This is also true for the DF-fus and DR-fusprimer sets. In addition, in some embodiments, these primers containrestriction enzyme sites similar to those used in Method 1 for use increating a plasmid vector (See, Table 3 and U.S. Pat. No. 5,023,171).Table 3 provides a list of primers useful for creation of deletionconstructs by PCR fusion. Table 4 provides an additional list of primersuseful for creation of deletion constructs by PCR fusion. However, inthis Table, all deletion constructs would include the phleo^(R) marker.TABLE 3 Primers Restriction enzyme engineered SEQ Primer name intoprimer Sequence ID. NO. DHB-UF XbaI CGAGAATCTAGAACAGGATGAATCATCTGTGGCGGG110 DHB-UFfus-phleo BamHI CGACTGTCCAGCCGCTCGGCACATCGGATCCGCTTA 111CCGAAAGCCAGACTCAGCAA DHB-URfus-phleo BamHITTGCTGAGTCTGGCTTTCGGTAAGCGGATCCGATGTG 112 CCGAGCGGCTGGACAGTCGDHB-DFfus-phleo BamHI CGTTAATGCGCCATGACAGCCATGAGGATCCCACAA 113GCCCGCACGCCTTGCCACAC DHB-DRfus-phleo BamHIGTGTGGCAAGGCGTGCGGGCTTGTGGGATCCTCATG 114 GCTGTCATGGCGCATTAACG DHB-DRSacI GACTTCGTCGACGAGTGCGGACGGCCAGCATCACCA 115 DHB-UF-nested XbaIGGCATATCTAGAGACATGAAGCGGGAAACAGATG 116 DHB-DR-nested SacIGGTGCGGAGCTCGACAGTATCACAGCCAGCGCTG 117 YvfF-yveK-UF XbaIAAGCGTTCTAGACTGCGGATGCAGATCGATCTCGGG 118 YvfF-yveK-UF- BamHIAACCTTCCGCTCACATGTGAGCAGGGGATCC 119 phleo GCTTACCGAAAGCCAGACTCAGCAAYvfF-yveK-UR- BamHI TTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 120 phleoCCTGCTCACATGTGAGCGGAAGGTT YvfF-yveK-DF- BamHICGTTAATGCGCCATGACAGCCATGAGGATCC 121 phleo GCCTTCAGCCTTCCCGCGGCTGGCTYvfF-yveK-DR- BamHI AGCCAGCCGCGGGAAGGCTGAAGGCGGATCC 122 phleoTCATGGCTGTCATGGCGCATTAACG YvfF-yveK-DR PstICAAGCACTGCAGCCCACACTTCAGGCGGCTCAGGTC 123 YvfF-yveK-UF- XbaIGAGATATCTAGAATGGTATGAAGCGGAATTCCCG 124 YvfF-yveK-DR- KpnIATAAACGGTACCCCCCTATAGATGCGAACGTTAGCCC 125 Prophage7-UF EcoRIAAGGAGGAATTCCATCTTGAGGTATACAAACAGTCAT 126 Prophage7-UF- BamHITCTCCGAGAAAGACAGGCAGGATCGGGATCC 127 Prophage7-UR- BamHITTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 128 Skin+prophage7- Asp718AAGGACGGTACCGGCTCATTACCCTCTTTTCAAGGGT 129 Skin+pro7-UF- BamHIACCAAAGCCGGACTCCCCCGCGAGAGGATCC 130 phleo GCTTACCGAAAGCCAGACTCAGCAASkin+pro7-UR- BamHI TTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 131 phleoTCTCGCGGGGGAGTCCGGCTTTGGT Skin+pro7-DF- BamHI CGTTAATGCGCCATGACAGCCATGA132 phleo GGATCCCATACGGGGTACACAATGTACCATA Skin+pro7-DR- BamHITATGGTACATTGTGTACCCCGTATGGGATCC 133 phleo TCATGGCTGTCATGGCGCATTAACGSkin+pro7-DR PstI GTCAACCTGCAGAGCGGCCCAGGTACAAGTTGGGGA 134 Skin+pro7-UF-SacI GGATCAGAGCTCGCTTGTCCTCCTGGGAACAGCCGG 135 Skin+pro7-DR- PstITATATGCTGCAGGGCTCAGACGGTACCGGTTGTTCCT 136

The restriction sites are designated as follows: XbaI is TCTAGA; BamHIis GGATCC, SacI is GAGCTC; Asp718 is GGTACC; PstI is CTGCAG and HindIIIis AAGCTT. TABLE 4 Additional Primers Used to Create Deletion Constructsby PCR Fusion*. Restriction Enzyme SEQ Engineered ID Primer Name IntoPrimer Sequence NO: Slr-UF XbaI CTGAACTCTAGACCTTCACCAGGCACAGAGGAGGTGA137 Slr-Uffus BamHI GCCAATAAGTTCTCTTAGAGAACAGGATCC 138GCTTACCGAAAGCCAGACTCAGCAA Slr-Urfus BamHITTGCTGAGTCTGGCTTTCGGTAAGCGGATCCTTGTTCTCT 139 AAAGAGAACTTATTGGC Slr-DffusBamHI CGTTAATGCGCCATGACAGCCATGAGGATCC 140 GGGCTAACGTTCGCATCTATAGGGGSlr-Drfus BamHI CCCCTATAGATGCGAACGTTAGCCC GGATCC 141 Slr-DR SacITGAGACGAGCTCGATGCATAGGCGACGGCAGGGCGCC 142 Slr-UF-nested XbaICGAAATTCTAGATCCCGCGATTCCGCCCTTTGTGG 143 Slr-DR-nested SacITTCCAAGAGCTCGCGGAATACCGGAAGCAGCCCC 144 YbcO-UF XbaICAATTCTCTAGAGCGGTCGGCGCAGGTATAGGAGGGG 145 YbcO-UF BamHIGAAAAGAAACCAAAAAGAATGGGAAGGATCC 146 GCTTACCGAAAGCCAGACTCAGCAA YbcO-URBamHI TTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 147 TTCCCATTCTTTTTGGTTTCTTTTCYbcO-DF BamHI CGTTAATGCGCCATGACAGCCATGAGGATCC 148GCTATTTAACATTTGAGAATAGGGA YbcO-DR BamHI TCCCTATTCTCAAATGTTAAATAGCGGATCC149 TCATGGCTGTCATGGCGCATTAACG YbcO-DR SacICAGGCGGAGCTCCCATTTATGACGTGCTTCCCTAAGC 150 Csn-UF XbaITACGAATCTAGAGATCATTGCGGAAGTAGAAGTGGAA 151 Csn-UF BamHITTTAGATTGAGTTCATCTGCAGCGGGGATCC 152 GCTTACCGAAAGCCAGACTCAGCAA Csn-URBamHI TTGCTGAGTCTGGCTTTGGGTAAGCGGATCC 153 CCGCTGCAGATGAACTCAATCTAAACsn-DF BamHI CGTTAATGCGCCATGACAGCCATGAGGATCC 154GCCAATCAGCCTTAGCCCCTCTCAC Csn-DR BamHI GTGAGAGGGGCTAAGGCTGATTGGCGGATCC155 TCATGGCTGTCATGGCGCATTAACG Csn-DR SalIATACTCGTCGACATACGTTGAATTGCCGAGAAGCCGC 156 Csn-UF- NACTGGAGTACCTGGATCTGGATCTCC 157 Csn-DR- NA GCTCGGCTTGTTTCAGCTCATTTCC 158SigB-UF SacI CGGTTTGAGCTCGCGTCCTGATCTGCAGAAGCTCATT 159 SigB-UF BamHICTAAAGATGAAGTCGATCGGCTCATGGATCC 160 GCTTACCGAAAGCCAGACTCAGCAA SigB-URBamHI TTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 161 ATGAGCCGATCGACTTCATCTTTAGSigB-DF BamHI CGTTAATGCGCCATGACAGCCATGAGGATCC 162GAAGATCCCTCGATGGAGTTAATGT SigB-DR BamHI ACATTAACTCCATCGAGGGATCTTCGGATCC163 TCATGGCTGTCATGGCGCATTAACG SigB-DR SalIGCTTCGGTCGACTTTGCCGTCTGGATATGCGTCTCTCG 164 SigB-UF- SacIGTCAAAGAGCTCTATGACAGCCTCCTCAAATTGCAGG 165 SigB-DR- SalITTCCATGTCGACGCTGTGCAAAACCGCCGGCAGCGCC 166 SpollSA-UF EcoRIACATTCGAATTCAGCAGGTCAATCAGCTCGCTGACGC 167 SpollSA-UF BamHICCAGCACTGCGCTCCCTCACCCGAAGGATCC 168 GCTTACCGAAAGCCAGACTCAGCAA SpollSA-URBamHI TTGCTGAGTCTGGCTTTCGGTAAGCGGATCC 169 TTCGGGTGAGGGAGCGCAGTGCTGGSpollSA-DF BamHI CGTTAATGCGCCATGACAGCCATGAGGATCC 170TCGAGAGATCCGGATGGTTTTCCTG SpollSA-DR BamHICAGGAAAACCATCCGGATCTCTCGAGGATCC 171 TCATGGCTGTCATGGCGCATTAACG SpollSA-DRHindIII AGTCAT AAGCTTTCTGGCGTTTGATTTCATCAACGGG 172 SpollSA-UF- NACAGCGCGACTTGTTAAGGGACAATA 173 SpollSA-DR- NA GGCTGCTGTGATGAACTTTGTCGGA174*All deletion constructs include the phleo^(R) marker

The fragments listed in Tables 3 and 4 were size-verified by gelelectrophoresis as described above. If correct, 1 μL each of theupstream, downstream, and antimicrobial resistance marker fragments wereplaced in a single reaction tube with the DeletionX-UF and DeletionX-DRprimers or nested primers where listed. Nested primers are 25 base pairsof DNA homologous to an internal portion of the upstream or downstreamfragment, usually about 100 base pairs from the outside end of thefragment (See, FIG. 2). The use of nested primers frequently enhancesthe success of fusion. The PCR reaction components were similar to thosedescribed above, except 82 μL of water was used to compensate foradditional template volume. The PCR reaction conditions were similar tothose described above, except the 72° C. extension was lengthened to 3minutes. During extension, the antimicrobial resistance gene was fusedin between the upstream and downstream pieces. This fusion fragment canbe directly transformed into Bacillus without any purification steps orwith a simple Qiagen Qiaquick PRC purification done according tomanufacturer's instructions.

Example 3 Creation of DNA Constructs Using Ligation of PCR Fragments andDirect Transformation of Bacillus subtilis to Bypass the E. coli CloningStep

In this Example, a method (“Method 3”) for creating DNA constructs usingligation of PCR fragments and direct transformation of Bacillus aredescribed. By way of example, modification of prpC, sigD and tdh/kbl areprovided to demonstrate the method of ligation. Indeed, sigD and tdh/kblwere constructed by one method and prpC by an alternate method.

A. Tdh/Kbl and SigD

The upstream and downstream fragments adjacent to the tdh/kbl region ofthe Bacillus subtilis chromosome were amplified by PCR similar to asdescribed in Method 1, except that the inside primer of the flanking DNAwas designed to contain type II s restriction sites. Primers for theloxP-spectinomycin-loxP cassette were designed with the same type II srestriction site as the flanks and complementary overhangs. Uniqueoverhangs for the left flank and the right flank allowed directionalligation of the antimicrobial cassette between the upstream anddownstream flanking DNA. All DNA fragments were digested with theappropriate restriction enzymes, and the fragments were purified with aQiagen Qiaquick PCR purification kit using the manufacturer'sinstructions. This purification was followed by desalting in a 1 mL spincolumn containing BioRad P-6 gel and equilibrated with 2 mM Tris-HCl, pH7.5. Fragments were concentrated to 124 to 250 ng/μL using a SavantSpeed Vac SC110 system. Three piece ligations of 0.8 to 1 μg of eachfragment were performed with 12U T4 ligase (Roche) in a 15 to 25 μLreaction volume at 14 to 16° C. for 16 hours. The total yield of thedesired ligation product was >100 ng per reaction, as estimated bycomparison to a standard DNA ladder on an agarose gel. The ligationmixture was used without purification for transformation reactions.Primers for this construction are shown in Table 5, below TABLE 5Primers for tdh/kbl Deletion Restriction Enzyme Engineered SEQ PrimerInto ID Name Primer Primer Sequence NO: p70 DR noneCTCAGTTCATCCATCAAATCACCAAGTCCG 175 P82 DF BbsITACACGTTAGAAGACGGCTAGATGCGTCTGATTGTGACAGAC 176 GGCG p71 UF noneAACCTTCCAGTCCGGTTTACTGTCGC 177 P83 UR BbsIGTACCATAAGAAGACGGAGCTTGCCGTGTCCACTCCGATTAT 178 AGCAG p98 spc F BbsICCTTGTCTTGAAGACGGAGCTGGATCCATAACTTCGTATAATG 179 p106 spc R BbsIGTACCATAAGAAGACGGCTAGAGGATGCATATGGCGGCCGC 180 p112 UF* noneCATATGCTCCGGCTCTTCAAGCAAG   (analytical primer) 181 p113 DR* noneCCTGAGATTGATAAACATGAAGTCCTC (analytical primer) 182*primers for analytical PCR

The construct for the sigD deletion closely followed construction oftdh/kbl. The primers used for the sigD construction are provided inTable 6. TABLE 6 Primers for sigD Construction Restriction EnzymeEngineered SEQ Primer Into ID Name Primer Primer Sequence NO: SigD UFnone ATATTGAAGTCGGCTGGATTGTGG 183 SigD UR BgIIIGCGGCAGATCTCGGCGCATTAAGTCG 184 TCA SigD DF EcoRIGCGGCGAATTCTCTGCTGGAAAAAGT 185 GATACA SigD DR none TTCGCTGGGATAACAACAT186 Loxspc UF BgIII GCGGCAGATCTTAAGCTGGATCCATA 187 ACTTCG Loxspc DREcoRI GCGGCGAATTCATATGGCGGCCGCAT 188 AACTTC SigD UO noneCAATTTACGCGGGGTGGTG 189 SigD DO none GAATAGGTTACGCAGTTGTTG 190 Spc URnone CTCCTGATCCAAACATGTAAG 191 Spc DF none AACCCTTGCATATGTCTAG 192

B. PrpC

An additional example of creating a DNA molecule by ligation of PCRamplified DNA fragments for direct transformation of Bacillus involved apartial in-frame deletion of the gene prpC. A 3953 bp fragment ofBacillus subtilis chromosomal DNA containing the prpC gene was amplifiedby PCR using primers p95 and p96. The fragment was cleaved at uniquerestriction sites PflMI and BstXI. This yielded three fragments, anupstream, a downstream, and a central fragment. The latter is thefragment deleted and consists of 170 bp located internal to the prpCgene. The digestion mixture was purified with a Qiagen Qiaquick PCRpurification kit, followed by desalting in a 1 mL spin column containingBioRad P-6 gel and equilibrated with 2 mM Tris-HCl, pH 7.5. In a secondPCR reaction, the antimicrobial cassette, loxP-spectinomycin-loxP, wasamplified with the primer containing a BstXI site and the downstreamprimer containing a PflMI site both with is cleavage sites complementaryto the sites in the genomic DNA fragment. The fragment was digested withPflMI and BstXI and purified as described for the chromosomal fragmentabove. A three piece ligation of the upstream, antimicrobial cassette,and the downstream fragments was carried out as for tdh/kbl, describedabove. The yield of desired ligation product was similar and theligation product was used without further treatment for thetransformation of xylRcomK competent Bacillus subtilis, as described ingreater detail below. TABLE 7 Primers for prpC Deletion RestrictionEnzyme Engineered SEQ Primer Into ID Name Primer Primer Sequence NO: p95none GCGCCCTTGATCCTAAGTCAGATGAA 193 DF AC p96 noneCGGGTCCGATACTGACTGTAAGTTTG 194 UR AC p100 PflMIGTACCATAACCATGCCTTGGTTAGGAT 195 spc R GCATATGGCGGCCGC p101 BstXICCTTGTCTTCCATCTTGCTGGAGCTGG 196 spc F ATCCATAACTTCGTATAATG p114 noneGAGAGCAAGGACATGACATTGACGC 197 anal. p115 noneGATCTTCACCCTCTTCAACTTGTAAAG 198 anal.,**anal., analytical PCR primer

C. PckA Deletion

In addition to the above deletions, pckA was also modified. The PCRprimers pckA F, pckA-2Urfus, spc ffus, spc rfus, pckA Dffus and pckA DR,were used for PCR and PCR fusion reactions using the chromosomal DNA ofa Bacillus subtilis 1168 derivative and pDG1726 (See, Guerout-Fleury etal., Gene 167(1-2):335-6 [1995]) as template. The primers are shown inTable 8. The method used in constructing these deletion mutants was thesame as Method 1, described above. TABLE 8 Primers Used for PckADeletion Restriction Enzyme Engineered Seq Primer Into ID Name PrimerPrimer Sequence NO: pckA UF none TTTGCTTCCTCCTGCACAAGGCC 199 TCpckA-2URfus none CGTTATTGTGTGTGCATTTCCAT 200 TGT spc ffus noneCAATGGAAATGCACACACAATAA 201 CGTGACTGGCAAGAGA pckA DFfus noneGTAATGGCCCTCTCGTATAAAAA 202 AC spc rfus none GTTTTTTATACGAGAGGGCCATT 203ACCAATTAGAATGAATATTTCCC pckA DR none GACCAAAATGTTTCGATTCAGCA 204 TTCCT

D. Xylose-Induced Competence Host Cell Transformation with Ligated DNA.

Cells of a host strain Bacillus subtilis with partial genotype xylRcomK,were rendered competent by growth for 2 hours in Luria-Bertani mediumcontaining 1% xylose, as described in U.S. patent application Ser. No.09/927,161, filed Aug. 10, 2001, herein incorporated by reference, to anOD₅₅₀ of 1. This culture was seeded from a 6 hour culture. All cultureswere grown at 37° C., with shaking at 300 rpm. Aliquots of 0.3 mL ofwere frozen as 1:1 mixtures of culture and 30% glycerol in round bottom2 mL tubes and stored in liquid nitrogen for future use.

For transformation, frozen competent cells were thawed at 37° C. andimmediately after thawing was completed, DNA from ligation reactionmixtures was added at a level of 5 to 15 μL per tube. Tubes were thenshaken at 1400 rpm (Tekmar VXR S-10) for 60 min at 37° C. Thetransformation mixture was plated without dilution in 100 uL aliquots on8 cm LA plates containing 100 ppm of spectinomycin. After growth overnight, transformants were picked into Luria-Bertani (100 ppmspectinomycin) and grown at 37° C. for genomic DNA isolation performedas known in the art (See e.g., Harwood and Cuttings, MolecularBiological Methods for Bacillus, John Wiley and Son, New York, N.Y.(1990], at p. 23). Typically 400 to 1400 transformants were obtainedfrom 100 uL transformation mix, when 5 uL of ligation reaction mix wasused in the transformation.

When the antimicrobial marker was located between two loxP sites in theincoming DNA, the marker could be removed by transforming the strainwith a plasmid containing the cre gene capable of expression the Creprotein. Cells were transformed with pCRM-TS-pleo (See below) culturedat 37° C. to 42° C., plated onto LA and after colonies formed patchedonto LA containing 100 ppm spectinomycin. Patches which did not growafter overnight incubation were deemed to have lost the antimicrobialmaker. Loss of maker was verified by PCR assay with primers appropriatefor the given gene. pCRM-TS-pleo has the following sequence: (SEQ IDNO:205) GGGGATCTCTGCAGTGAGATCTGGTAATGACTCTCTAGCTTGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCTCTAGCTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTGTTAACTCTAGAGCTGCCTGCCGCGTTTCGGTGATGAAGATCTTCCCGATGATTAATTAATTCAGAACGCTCGGTTGCCGCCGGGCGTTTTTTATGCAGCAATGGCAAGAACGTTGCTCTAGAATAATTCTACACAGCCCAGTCCAGACTATTCGGCACTGAAATTATGGGTGAAGTGGTCAAGACCTCACTAGGCACCTTAAAAATAGCGCACCCTGAAGAAGATTTATYTGAGGTAGCCCTTGCCTACCTAGCTTCCAAGAAAGATATCCTAACAGCACAAGAGCGGAAAGATGTTTTGTTCTACATCCAGAACAACCTCTGCTAAAATTCCTGAAAAATTTTGCAAAAAGTTGTTGACTTTATCTACAAGGTGTGGCATAATGTGTGGAATTGTGAGCGGATAACAATTAAGCTTAGGAGGGAGTGTTAAATGTCCAATTTACTGACCGTACACCAAAATTTGCCTGCATTACCGGTCGATGCAACGAGTGATGAGGTTCGCAAGAACCTGATGGACATGTTCAGGGATCGCCAGGCGTTTTCTGAGCATACCTGGAAAATGCTTCTGTCCGTTTGCCGGTCGTGGGCGGCATGGTGCAAGTTGAATAACCGGAAATGGTTTCCCGCAGAACCTGAAGATGTTCGCGATTATCTTCTATATCTTCAGGCGCGCGGTCTGGCAGTAAAAACTATCCAGCAACATTTGGGCCAGCTAAACATGCTTCATCGTCGGTCCGGGCTGCCACGACCAAGTGACAGCAATGCTGTTTCACTGGTTATGCGGCGGATCGGAAAAGAAAACGTTGATGCCGGTGAACGTGCAAAACAGGCTCTAGCGTTCGAACGCACTGATTTCGACCAGGTTCGTTCACTCATGGAAAATAGCGATCGCTGCCAGGATATACGTAATCTGGCATTTCTGGGGATTGCTTATAACACCCTGTTACGTATAGCCGAAATTGCCAGGATCAGGGTTAAAGATATCTCACGTACTGACGGTGGGAGAATGTTAATCCATATTGGCAGAACGAAAACGCTGGTTAGCACCGCAGGTGTAGAGAAGGCACTTAGCCTGGGGGTAACTAAACTGGTCGAGCGATGGATTTCCGTCTCTGGTGTAGCTGATGATCCGAATAACTACCTGTTTTGCCGGGTCAGAAAAAATGGTGTTGCCGCGCCATCTGCCACCAGCCAGCTATCAACTCGCGCCCTGGAAGGGATTTTTGAAGCAACTCATCGATTGATTTACGGCGCTAAGGATGACTCTGGTCAGAGATACCTGGCCTGGTCTGGACACAGTGCCCGTGTCGGAGCCGCGCGAGATATGGCCCGCGCTGGAGTTTCAATACCGGAGATCATGCAAGCTGGTGGCTGGACCAATGTAAATATTGTCATGAACTATATCCGTAACCTGGATAGTGAAACAGGGGCAATGGTGCGCCTGCTGGAAGATGGCGATTAGGAGCTCGCATCACACGCAAAAAGGAAATTGGAATAAATGCGAAATTTGAGATGTTAATTAAAGACCTTTTTGAGGTCTTTTTTTCTTAGATTTTTGGGGTTATTTAGGGGAGAAAACATAGGGGGGTACTACGACCTCCCCCCTAGGTGTCCATTGTCCATTGTCCAAACAAATAAATAAATATTGGGTTTTTAATGTTAAAAGGTTGTTTTTTATGTTAAAGTGAAAAAAACAGATGTTGGGAGGTACAGTGATAGTTGTAGATAGAAAAGAAGAGAAAAAAGTTGCTGTTACTTTAAGACTTACAACAGAAGAAAATGAGATATTAAATAGAATCAAAGAAAAATATAATATTAGCAAATCAGATGCAACCGGTATTCTAATAAAAAAATATGCAAAGGAGGAATACGGTGCATTTTAAACAAAAAAAGATAGACAGCACTGGCATGCTGCCTATCTATGACTAAATTTTGTTAAGTGTATTAGCACCGTTATTATATCATGAGCGAAAATGTAATAAAAGAAACTGAAAACAAGAAAAATTCAAGAGGACGTAATTGGACATTTGTTTTATATCCAGAATCAGCAAAAGCCGAGTGGTTAGAGTATTTAAAAGAGTTACACATTCAATTTGTAGTGTCTCCATTACATGATAGGGATACTGATACAGAAGGTAGGATGAAAAAAGAGCATTATCATATTCTAGTGATGTATGAGGGTAATAAATCTTATGAACAGATAAAAATAATTAACAGAAGAATTGAATGCGACTATTCCGCAGATTGCAGGAAGTGTGAAAGGTCTTGTGAGATATATGCTTCACATGGACGATCCTAATAAATTTAAATATCAAAAAGAAGATATGATAGTTTATGGCGGTGTAGATGTTGATGAATTATTAAAGAAAACAACAAGAGATAGATATAAATTAATTAAAGAAATGATAGAGTTTATTGATGAACAAGGAATCGTAGAATTTAAGAGTTTAATGGATTATGCAATGAAGTTTAAATTTGATGATTGGTTCCCGCTTTTATGTGATAACTCGGCGTATGTTATTCAAGAATATATAAAATCAAATCGGTATAAATCTGACCGATAGATTTTGAATTTAGGTGTCACAAGACACTCTTTTTTCGCACCAGCGAAAACTGGTTTAAGCCGACTGGAGCTCCTGCACTGGATGGTGGCGCTGGATGGTAAGCCGCTGGCAAGCGGTGAAGTGCCTCTGGATGTCGCTCCACAAGGTAAACAGTTGATTGAACTGCCTGAACTACCGCAGCCGGAGAGCGCCGGGCAACTCTGGCTCACAGTACGCGTAGTGCAACCGAACGCGAGCGCATGGTCAGAAGCCGGGCACATCAGCGCCTGGCAGCAGTGGCGTCTGGCGGAAAACCTCAGTGTGACGCTCCCCGCCGCGTCCCACGCCATCCCGCATCTGACCACCAGCGAAATGGATTTTTGCATCGAGCTGGGTAATAAGCGTTGGCAATTTAACCGCCAGTCAGGCTTTCTTTCACAGATGTGGATTGGCGATAAAAAACAACTGCTGACGCCGCTGCGCGATCAGTTCACCCGTGCACCGCTGGATAACGACATTGGCGTAAGTGAAGCGACCCGCATTGACCCTAACGCCTGGGTCGAACGCTGGAAGGCGGCGGGCCATTACCAGGCCGAAGCAGCGTTGTTGCAGTGCACGGCAGATACACTTGCTGATGCGGTGCTGATTACGACCGCTCACGCGTGGCAGCATCAGGGGAAAACCTTATTTATCAGCCGGAAAACCTACCGGATTGATGGTAGTGGTCAAATGGCGATTACCGTTGATGTTGAAGTGGCGAGCGATACACCGCATCCGGCGCGGATTGGCCTGAACTGCCAGCTGGCGCAGGTAGCAGAGCGGGTAAACTGGCTCGGATTAGGGCCGCAAGAAAACTATCCCGACCGCCTTACTGCCGCCTGTTTTGACCGCTGGGATCTGCCATTGTCAGACATGTATACCCCGTACGTCTTCCCGAGCGAAAACGGTCTGCGCTGCGGGACGCGCGAATTGAATTATGGCCCACACCAGTGGCGCGGCGACTTCCAGTTCAACATCAGCCGCTACAGTCAACAGCAACTGATGGAAACCAGCCATCGCCATCTGCTGCACGCGGAAGAAGGCACATGGCTGAATATCGACGGTTTCCATATGGGGATTGGTGGCGACGACTCCTGGAGCCCGTCAGTATCGGCGGAATTCCAGCTGAGCGCCGGTCGCTACCATTACCAGTTGGTCTGGTGTCAAAAATAATAATAACCGGGCAGGCCATGTCTGCCCGTATTTCGCGTAAGGAAATCCATTATGTACTATTACAAGCTAATTCCGGTGGAAACGAGGTCATCATTTCCTTCCGAAAAAACGGTTGCATTTAAATCTTACATATGTAATACTTTCAAAGACTACATTTGTAAGATTTGATGTTTGAGTCGGCTGAAAGATCGTACGTACCAATTATTGTTTCGTGATTGTTCAAGCCATAACACTGTAGGGATAGTGGAAAGAGTGCTTCATCTGGTTACGATCAATCAAATATTCAAACGGAGGGAGACGATTTTGATGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTCCCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCACCTCCAGTCTGGCCCTGCACGCGCCGTCGCAAATTGTCGCGGCGATTAAATCTCGCGCCGATCAACTGGGTGCCAGCGTGGTGGTGTCGATGGTAGAACGAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCTTCTCGCGCAACGCGTCAGTGGGCTGATCATTAACTATCCGCTGGATGACCAGGATGCCATTGCTGTGGAAGCTGCCTGCACTAATGTTCCGGCGTTATTTCTTGATGTCTCTGACCAGACACCCATCAACAGTATTATTTTCTCCCATGAAGACGGTACGCGACTGGGCGTGGAGCATCTGGTCGCATTGGGTCACCAGCAAATCGCGCTGTTAGCGGGCCCATTAAGTTCTGTCTCGGCGCGTCTGCGTCTGGCTGGCTGGCATAAATATCTCACTCGCAATCAAATTCAGCCGATAGCGGAACGGGAAGGCGACTGGAGTGCCATGTCCGGTTTTCAACAAACCATGCAAATGCTGAATGAGGGCATCGTTCCCACTGCGATGCTGGTTGCCAACGATCAGATGGCGCTGGGCGCAATGCGCGCCATTACCGAGTCCGGGCTGCGCGTTGGTGCGGATATCTCGGTAGTGGGATACGACGATACCGAAGACAGCTCATGTTATATCCCGCCGTCAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTGACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGGCATCGCATCCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTGCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCAATGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTAAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGAATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCCAATAGACCAGTTGCAATCCAAACGAGAGTCTAATAGAATGAGGTCGAAAAGTAAATCGCGTAATAAGGTAATAGATTTACATTAGAAAATGAAAGGGGATTTTATGCGTGAGAATGTTAGAGTCTATCCCGGCATTGCCAGTCGGGGATATTAAAAAGAGTATAGGTTTTTATTGCGATAAACTAGGTTTCACTTTGGTTCACCATGAAGATGGATTCGCAGTTCTAATGTGTAATGAGGTTCGGATTCATCTATGGGAGGCAAGTGATGAAGGCTGGCGCTCTCGTAGTAATGATTCACCGGTTTGTACAGGTGCGGAGTCGTTTATTGCTGGTACTGCTAGTTGCCGCATTGAAGTAGAGGGAATTGATGAATTATATCAACATATTAAGCCTTTGGGCATTTTGCACCCCAATACATCATTAAAAGATCAGTGGTGGGATGAACGAGACTTTGCAGTAATTGATCCCGACAACAATTTGATTACAAATAAAAAGCTAAAATCTATTATTAATCTGTTCCTGCAGGAGAGACCG

E. Transcriptome DNA Array Methods

In addition to the above methods, transcriptome DNA array methods wereused in the development of mutants of the present invention. First,target RNA was harvested from a Bacillus strain by guanidinium acidphenol extraction as known in the art (See e.g., Farrell, RNAMethodologies, (2nd Ed.). Academic Press, San Diego, at pp. 81] andtime-point was reverse-transcribed into biotin-labeled cDNA by a methodadopted from deSaizieu et al. (deSaizieu et al., J. Bacteriol., 182:4696-4703 [2000]) and described herein. Total RNA (25 mg) was incubated37° C. overnight in a 100-mL reaction: 1×GIBCO first-strand buffer (50mM Tris-HCl pH 8.3, 75 mM KCl, 3 mM MgCl₂); 10 mM DTT; 40 mM randomhexamer; 0.3 mM each dCTP, dGTP and dTTP; 0.12 mM dATP; 0.3 mMbiotin-dATP (NENO; 2500 units SuperScript II reverse-transcriptase(Roche). To remove RNA, the reaction was brought to 0.25 M NaOH andincubated at 65° C. for 30 minutes. The reaction was neutralized withHCl and the nucleic acid precipitated at −20° C. in ethanol with 2.5 Mammonium-acetate. The pellet was washed, air-dried, resuspended inwater, and quantitated by UV spectroscopy. The reaction yield wasapproximately 20-25 mg biotin-labeled cDNA.

Twelve mg of this cDNA were fragmented in 33 mL 1× One-Phor-All buffer(Amersham-Pharmacia #27-0901-02) with 3.75 milliunits of DNasel I at 37°C. for 10 minutes. After heat-killing the DNase, fragmentation wasvalidated by running 2 mg of the fragmented cDNA on a 3% agarose gel.Biotin-containing cDNA routinely ranged in size from 25 to 125nucleotides. The remaining 10 mg of cDNA were hybridized to anAffymetrix Bacillus GeneChip array.

Hybridizations were performed as described in the Affymetrix ExpressionAnalysis Technical Manual (Affymetrix) using reagent suppliers assuggested. Briefly, 10 mg of fragmented biotin-labeled cDNA were addedto a 220-mL hybridization cocktail containing: 100 mM MES(N-morpholinoethanesufonic acid), 1M Na⁺, 20 mM EDTA, 0.01% Tween 20; 5mg/mL total yeast RNA; 0.5 mg/mL BSA; 0.1 mg/mL herring-sperm DNA; 50 pMcontrol oligonucleotide (AFFX-B1). The cocktails were heated to 95° C.for 5 minutes, cooled to 40° C. for 5 minutes, briefly centrifuged toremove particulates, and 200 mL was injected into each pre-warmedpre-rinsed (1×MES buffer+5 mg/ml yeast RNA) GeneChip cartridge. Thearrays were rotated at 40° C. overnight.

The samples were removed and the arrays were filled with non-stringentwash buffer (6×SSPE, 0.01% Tween 20) and washed on the Affymetrixfluidics station with protocol Euk-GE-WS2, using non-stringent andstringent (0.1 M MES, 0.1 M [Na⁺], 0.01% Tween 20) wash buffers. Arrayswere stained in three steps: (1) streptavidin; (2) anti-streptavidinantibody tagged with biotin; (3) streptavidin-phycoerythrin conjugate.

The signals in the arrays were detected with the Hewlett-Packard GeneArray Scanner using 570 nm laser light with 3-mm pixel resolution. Thesignal intensities of the 4351 ORF probe sets were scaled and normalizedacross all time points comprising a time course experiment. Thesesignals were then compared to deduce the relative expression levels ofgenes under investigation. The threonine biosynthetic and degradativegenes were simultaneous transcribed, indicating inefficient threonineutilization. Deletion of the degradative threonine pathway improvedexpression of the desired product (See, FIG. 7). The present inventionprovides means to modify pathways with transcription profiles that aresimilar to threonine biosynthetic and degradative profiles. Thus, thepresent invention also finds use in the modification of pathways withtranscription profiles similar to threonine in order to optimizeBacillus strains. In some preferred embodiments, at least one geneselected from the group consisting of rocA, ycgN, ycgM rocF and rocD isdeleted or otherwise modified. Using the present invention as describedherein resulted in the surprising discovery that the sigD regulon wastranscribed. Deletion of this gene resulted in better expression of thedesired product (See, FIG. 7). It was also surprising to find thetranscription of gapB and pckA. Deletion of pckA did not result inimprovement or detriment. However, the present invention provides meansto improve strain protein production through the combination of pckAdeletion or modification and deletion or modification of gapB and/orfbp. In addition, during the development of the present invention, itwas observed that the tryptophan biosynthetic pathway genes showedunbalanced transcription. Thus, it is contemplated that the presentinvention will find use in producing strains that exhibit increasedtranscription of genes such as those selected from the group consistingof trpA, trpB, trpC, trpD, trpE, and/or trpF, such that the improvedstrains provide improved expression of the desired product, as comparedto the parental (i.e., wild-type and/or originating strain). Indeed, itis contemplated that modifications of these genes in any combinationwill lead to improved expression of the desired product.

F. Fermentations

Analysis of the strains produced using the above constructs wereconducted following fermentation. Cultures at 14 L scale were conductedin Biolafitte® fermenters. Media components per 7 liters are listed inTable 9. TABLE 9 Media Components per 7L Fermentation NaH2PO4-H2O  0.8%  56 g KH2PO4  0.8%   56 g MgSO4-7H2O 0.28% 19.6 g antifoam  0.1%   7 gCaCl2-2H2O 0.01%  0.7 g ferrous sulfate-7H2O 0.03%  2.1 g MnCl2-4H2O0.02%  1.4 g trace metals 100 ×   1%   70 g stock* H2SO4 0.16% 11.2 g60% glucose 1.29%   90*See, Harwood and Cutting, supra, at p. 549

The tanks were stirred at 750 rpm and airflow was adjusted to 11 Litersper minute, the temperature was 37° C., and the pH was maintained at 6.8using NH₄OH. A 60% glucose solution was fed starting at about 14 hoursin a linear ramp from 0.5 to 2.1 grams per minute to the end of thefermentation. Off-gasses were monitored by mass spectrometry. Carbonbalance and efficiency were calculated from glucose fed, yield ofprotein product, cell mass yield, other carbon in broth, and CO₂evolved. A mutant strain was compared to parent strain to judgeimprovements. Although this mutant pckA strain did not show improvementunder these conditions, it is contemplated that improvements will beproduced under modified culture conditions (i.e., as known to those inthe art), and/or incorporation of additional genes. In some preferredembodiments, these additional genes are selected from the groupconsisting of gapB, alsD, and/or fbp

Example 4 Host Cell Transformation to Obtain an Altered Bacillus Strain

Once the DNA construct was created by Method 1 or 2 as described above,it was transformed into a suitable Bacillus subtilis lab strain (e.g.,BG2036 or BG2097; any competent Bacillus immediate host cell may be usedin the methods of the present invention). The cells were plated on aselective media of 0.5 ppm phleomycin or 100 ppm spectinomycin asappropriate (Ferrari and Miller, Bacillus Expression: A Gram-PositiveModel in Gene Expression Systems: Using Nature for the Art ofExpression, pgs 65-94 [1999]). The laboratory strains were used as asource of chromosomal DNA carrying the deletion that was transformedinto a Bacillus subtilis production host strain twice or BG3594 and thenMDT 98-113 once. Transformants were streaked to isolate a single colony,picked and grown overnight in 5 mL of LB plus the appropriateantimicrobial. Chromosomal DNA was isolated as known in the art (Seee.g., Hardwood et al., supra).

The presence of the integrated DNA construct was confirmed by three PCRreactions, with components and conditions as described above. Forexample, two reactions were designed to amplify a region from outsidethe deletion cassette into the antimicrobial gene in one case (primers 1and 11) and through the entire insert in another (primers 1 and 12). Athird check amplified a region from outside the deletion cassette intothe deleted region (primers 1 and 4). FIG. 4 shows that a correct cloneshowed a band in the first two cases but not the third. Wild-typeBacillus subtilis chromosomal DNA was used as a negative control in allreactions, and should only amplify a band with the third primer set.

Example 5 Shake Flask Assays—Measurement of Protease Activity

Once the DNA construct was stably integrated into a competent Bacillussubtilis strain, the subtilisin activity was measured by shake flaskassays and the activity was compared to wild type levels. Assays wereperformed in 250 ml baffled flasks containing 50 mL of growth mediasuitable for subtilisin production as known in the art (See,Christianson et al., Anal. Biochem., 223:119-129 [1994]; and Hsia etal., Anal. Biochem. 242:221-227 [1996]). The media were inoculated with50 μL of an 8 hour 5 mL culture and grown for 40 hours at 37° C. withshaking at 250 RPM. Then, 1 mL samples were taken at 17, 24 and 40 hoursfor protease activity assays. Protease activity was measured at 405 nMusing the Monarch Automatic Analyser. Samples in duplicate were diluted1:11 (3.131 g/L) in buffer. As a control to ensure correct machinecalibration one sample was diluted 1:6 (5.585 g/L), 1:12 (2.793 g/L and1:18 (1.862 g/L). FIG. 7 illustrates the protease activity in variousaltered Bacillus subtilis clones. FIG. 8 provides a graph showingimproved protease secretion as measured from shake flask cultures inBacillus subtilis wild-type strain (unaltered) and corresponding altereddeletion strains (−sbo) and (−slr). Protease activity (g/L) was measuredafter 17, 24 and 40 hours.

Cell density was also determined using spectrophotometric measurement atan OD of 600. No significant differences were observed for the samplesat the measured time (data not shown).

All publications and patents mentioned in the above specification areherein incorporated by reference. Various modifications and variationsof the described method and system of the invention will be apparent tothose skilled in the art without departing from the scope and spirit ofthe invention. Although the invention has been described in connectionwith specific preferred embodiments, it should be understood that theinvention as should not be unduly limited to such specific embodiments.Indeed, various modifications of the described modes for carrying outthe invention that are obvious to those skilled in the art and/orrelated fields are intended to be within the scope of the presentinvention.

1. A method for enhancing expression of a protein of interest fromBacillus comprising: a) obtaining an altered Bacillus strain capable ofproducing a protein of interest, wherein said altered Bacillus strainhas at least one inactivated chromosomal gene selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS,trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB,pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD; and b) growing said alteredBacillus strain under conditions such that said protein of interest isexpressed by said altered Bacillus strain, wherein said expression ofsaid protein of interest is enhanced compared to the expression of saidprotein of interest in an unaltered Bacillus host strain.
 2. The methodof claim 1, wherein said protein of interest is selected from the groupconsisting of homologous proteins and heterologous proteins.
 3. Themethod of claim 1, wherein said protein of interest is an enzymeselected from the group consisting of proteases, cellulases, amylases,carbohydrases, lipases, isomerases, transferases, kinases, andphosphatases.
 4. The method of claim 3, wherein said protein of interestis a protease.
 5. The method of claim 1, wherein said altered Bacillusstrain is obtained by deleting one or more chromosomal genes selectedfrom the group consisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC,rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD,prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD.
 6. An alteredBacillus strain obtained using the method of claim
 1. 7. An alteredBacillus strain comprising a chromosomal deletion of one or more genesselected from the group consisting of sbo, slr, ybcO, csn, spoIISA,sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl,alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD. 8.The altered Bacillus strain of claim 7, wherein said altered strain is aB. subtilis strain.
 9. The altered Bacillus strain of claim 7, whereinsaid altered Bacillus strain is a protease producing strain.
 10. Thealtered Bacillus strain of claim 9, wherein said protease is asubtilisin.
 11. The altered Bacillus strain of claim 11, wherein saidsubtilisin is selected from the group consisting of subtilisin 168,subtilisin BPN′, subtilisin Carlsberg, subtilisin DY, subtilisin 147,subtilisin 309 and variants thereof.
 12. The altered Bacillus strain ofclaim 7, wherein said altered Bacillus strain further comprises amutation in a gene selected from the group consisting of degU, degQ,degS, scoC4, spoIIE, and oppA.
 13. The altered Bacillus strain of claim7, wherein said altered Bacillus strain further comprises a heterologousprotein of interest.
 14. A DNA construct comprising at least one geneselected from the group consisting of sbo, slr, ybcO, csn, spoIISA,sigB, phrC, rapA, CssS, trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl,alsD, sigD, prpC, gapB, pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD,gene fragments thereof, and homologous sequences thereto.
 15. The DNAconstruct of claim 14, wherein said at least one gene comprises at leastone nucleic acid sequence selected from the group consisting of SEQ IDNO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ IDNO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:39, SEQ IDNO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ IDNO:50, SEQ ID NO:37, SEQ ID NO:25, SEQ ID NO:21, SEQ ID NO:50, SEQ IDNO:29, SEQ ID NO:23, SEQ ID NO:27, SEQ ID NO:19, SEQ ID NO:31, SEQ IDNO:48, SEQ ID NO:46, SEQ ID NO:35, and SEQ ID NO:33.
 16. The DNAconstruct of claim 14, wherein said construct further comprises apolynucleotide sequence encoding a protein of interest.
 17. A plasmidcomprising the DNA construct of claim
 16. 18. A host cell comprising theplasmid of claim
 17. 19. The host cell of claim 18, wherein said hostcell is selected from the group consisting of Bacillus cells and E. colicells.
 20. The host cell of claim 19, wherein said host cell is B.subtilis.
 21. The host cell of claim 18, wherein said DNA construct hasbeen integrated into the chromosome of said host cell.
 22. The DNAconstruct of claim 14, wherein said at least one gene encodes at leastone amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO:12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO:18, SEQ ID NO:41, SEQ IDNO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ IDNO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ ID NO:57, SEQ ID NO:30, SEQ IDNO:24, SEQ ID NO:28, SEQ ID NO:20, SEQ ID NO:32, SEQ ID NO:55, SEQ IDNO:53, SEQ ID NO:36, and SEQ ID NO:34.
 23. The DNA construct of claim14, further comprising a selective marker, wherein the selective markeris flanked on each side by a fragment of said gene or homologous genesequence thereto.
 24. A DNA construct comprising an incoming sequence,wherein said incoming sequence comprises a nucleic acid encoding aprotein of interest, and a selective marker flanked on each side with ahomology box, wherein said homology box includes nucleic acid sequenceshaving 80 to 100% sequence identity to the sequence immediately flankingthe coding regions of at least one gene selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS,trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB,pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD.
 25. The DNA construct ofclaim 24, further comprising at least one nucleic acids which flanks thecoding sequence of said gene.
 26. A plasmid comprising the DNA constructof claim
 25. 27. A host cell comprising the plasmid of claim
 26. 28. Thehost cell of claim 27, wherein said host cell is selected from the groupconsisting of Bacillus cells and E. coli cells.
 29. The host cell ofclaim 28, wherein said host cell is B. subtilis.
 30. The host cell ofclaim 26, wherein said DNA construct has been integrated into the hostcell chromosome.
 31. The host cell of claim 30, wherein said selectivemarker has been excised from said host cell chromosome.
 32. A method forobtaining an altered Bacillus strain with enhanced protease productioncomprising: a) transforming a Bacillus host cell with the DNA constructof claim 14, wherein said protein of interest in said DNA construct is aprotease, and wherein said DNA construct is integrated into thechromosome of the Bacillus host cell under conditions such that said atleast one gene is inactivated to produce an altered Bacillus strain; andb) growing said altered Bacillus strain under conditions such thatenhanced protease production is obtained.
 33. The method of claim 32,further comprising recovering said protease.
 34. The method of claim 32,wherein said at least one inactivated gene is deleted from thechromosome of said altered Bacillus strain.
 35. An altered Bacillusstrain produced using the method of claim
 32. 36. The method of claim33, wherein said Bacillus host strain is selected from the groupconsisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. alkalophilus, B.coagulans, B. circulans, B. pumilus, B. lautus, B. clausii, B.megaterium, and B. thuringiensis.
 37. The method of claim 36, whereinsaid Bacillus host cell is B. subtilis.
 38. A method for enhancingexpression of a protease in an altered Bacillus comprising: a)transforming a Bacillus host cell with the DNA construct of claim 24; b)allowing homologous recombination of said DNA construct and a region ofthe chromosome of said Bacillus host cell, wherein at least one gene ofsaid chromosome of said Bacillus host cell is inactivated, to produce analtered Bacillus strain; and c) growing said altered Bacillus strainunder conditions suitable for the expression of said protease, whereinthe production of said protease is greater in the altered Bacillussubtilis strain compared to said Bacillus subtilis host prior totransformation in step a).
 39. The method of claim 38, wherein saidprotease is subtilisin.
 40. The method of claim 38, wherein saidprotease is a recombinant protease.
 41. The method of claim 38, whereinsaid inactivation is by deletion of at least one of said genes.
 42. Themethod of claim 38, wherein said inactivation is by insertionalinactivation of said at least one of said genes.
 43. The alteredBacillus strain obtained using the method of claim
 38. 44. The alteredBacillus strain of claim 38, wherein said altered Bacillus straincomprises at least one inactivated gene selected from the groupconsisting of sbo, slr, ybcO, csn, spoIISA, sigB, phrC, rapA, CssS,trpA, trpB, trpC, trpD, trpE, trpF, tdh/kbl, alsD, sigD, prpC, gapB,pckA, fbp, rocA, ycgN, ycgM, rocF, and rocD.
 45. The altered Bacillusstrain of claim 44, wherein said inactivated gene has been inactivatedby deletion.
 46. The altered Bacillus strain of claim 44, furthercomprising at least one mutation in a gene selected from the groupconsisting of degU, degS, degQ, scoC4, spoIIE, and oppA.
 47. The alteredBacillus strain of claim 46, wherein said mutation is degU(Hy)32. 48.The altered Bacillus strain of claim 44, wherein said strain is arecombinant protease producing strain.
 49. The altered Bacillus strainof claim 44, wherein said altered Bacillus strain is selected from thegroup consisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. alkalophilus, B.coagulans, B. circulans, B. pumilus, B. lautus, B. clausii, B.megaterium, and B. thuringiensis.
 50. An altered Bacillus straincomprising a deletion of one or more indigenous chromosomal regions orfragments thereof, wherein said indigenous chromosomal region includesabout 0.5 to 500 kb, and wherein said altered Bacillus strain has anenhanced level of expression of a protein of interest compared to acorresponding unaltered Bacillus strain when said altered and unalteredBacillus strains are grown under essentially the same growth conditions.51. The altered Bacillus strain of claim 50, wherein said alteredBacillus strain is selected from the group consisting of B.licheniformis, B. lentus, B. subtilis, B. amyloliquefaciens B. brevis,B. stearothermophilus, B. alkalophilus, B. coagulans, B. circulans, B.pumilus, B. lautus, B. clausii, B. megaterium, and B. thuringiensis. 52.The altered Bacillus strain of claim 51, wherein said altered Bacillusstrain is selected from the group consisting of B. subtilis, B.licheniformis, and B. amyloliquefaciens.
 53. The altered Bacillus strainof claim 52, wherein said altered Bacillus strain is a B. subtilisstrain.
 54. The altered Bacillus strain of claim 50, wherein saidindigenous chromosomal region is selected from the group consisting of aPBSX region, a skin region, a prophage 7 region, a SPβ region, aprophage 1 region, a prophage 2 region, a prophage 4 region, a prophage3 region, a prophage 4 region, a prophage 5 region, a prophage 6,region, a PPS region, a PKS region, a YVFF-YVEK region, a DHB region andfragments thereof.
 55. The altered Bacillus strain of claim 50, whereintwo indigenous chromosomal regions or fragments thereof have beendeleted.
 56. The altered Bacillus strain of claim 50, wherein saidprotein of interest is a protease.
 57. The altered Bacillus strain ofclaim 56, wherein said protease is a subtilisin.
 58. The alteredBacillus strain of claim 57, wherein said subtilisin is selected fromthe group consisting of subtilisin 168, subtilisin BPN′, subtilisinCarlsberg, subtilisin DY, subtilisin 147 and subtilisin 309 and variantsthereof.
 59. The altered Bacillus strain of claim 50, wherein saidBacillus host is a recombinant strain.
 60. The altered Bacillus strainof claim 50, further comprising at least one mutation in a gene selectedfrom the group consisting of degU, degQ, degS, sco4, spoIIE and oppA.61. A protease producing Bacillus strain comprising a deletion of anindigenous chromosomal region selected from the group consisting of aPBSX region, a skin region, a prophage 7 region, a SPβ region, aprophage 1 region, a prophage 2 region, a prophage 3 region, a prophage4 region, a prophage 5 region, a prophage 6 region, a PPS region, a PKSregion, a YVFF-YVEK region, a DHB region and fragments thereof.
 62. Theprotease producing Bacillus strain of claim 61, wherein said protease isa subtilisin.
 63. The protease producing Bacillus strain of claim 62,wherein said Bacillus is a B. subtilis strain.
 64. The proteaseproducing Bacillus strain of claim 61, wherein said protease is aheterologous protease.
 65. A method for enhancing the expression of aprotein of interest in Bacillus comprising: a) introducing a DNAconstruct including a selective marker and an inactivating chromosomalsegment into a Bacillus host strain, wherein said DNA construct isintegrated into the chromosome of said Bacillus host strain, resultingin the deletion of an indigenous chromosomal region or fragment thereoffrom said Bacillus host cell to produce an altered Bacillus strain; andb) growing said altered Bacillus strain under suitable conditions,wherein expression of a protein of interest is greater in the alteredBacillus strain compared to the expression of the protein of interest ina Bacillus host cell that has not been altered.
 66. The method of claim65, further comprising recovering said protein of interest.
 67. Themethod of claim 65, further comprising the step of excising saidselective marker from the altered Bacillus strain.
 68. The method ofclaim 65, wherein said indigenous chromosomal region is selected fromthe group of regions consisting of PBSX, SKIN, prophage 7, SPβ, prophage1, prophage 2, prophage 3, prophage 4, prophage 5, prophage 6, PPS, PKS,YVFF-YVEK, DHB and fragments thereof.
 69. The method of claim 65,wherein said altered Bacillus strain comprises deletion of at least twoindigenous chromosomal regions.
 70. The method of claim 65, wherein saidprotein of interest is an enzyme.
 71. The method of claim 65, whereinsaid Bacillus host strain is selected from the group consisting of B.licheniformis, B. lentus, B. subtilis, B. amyloliquefaciens B. brevis,B. stearothermophilus, B. clausii, B. alkalophilus, B. coagulans, B.circulans, B. pumilus and B. thuringiensis.
 72. An altered Bacillusstrain produced using the method of claim
 65. 73. A method for obtaininga protein of interest from a Bacillus strain comprising: a) transforminga Bacillus host cell with a DNA construct comprising a selective markerand an inactivating chromosomal segment, wherein said DNA construct isintegrated into the chromosome of the Bacillus strain resulting indeletion of an indigenous chromosomal region or fragment thereof, toproduce an altered Bacillus strain, b) culturing said altered Bacillusstrain under suitable growth conditions to allow the expression of aprotein of interest, and c) recovering said protein of interest.
 74. Themethod of claim 73, wherein said protein of interest is an enzyme. 75.The method of claim 73, wherein said Bacillus host comprises aheterologous gene encoding a protein of interest.
 76. The method ofclaim 73, wherein said Bacillus host cell is selected from the groupconsisting of B. licheniformis, B. lentus, B. subtilis, B.amyloliquefaciens B. brevis, B. stearothermophilus, B. clausii B.alkalophilus, B. coagulans, B. circulans, B. pumilus and B.thuringiensis.
 77. The method of claim 73, wherein said indigenouschromosomal region is selected from the group of regions consisting ofPBSX, SKIN, prophage 7, SPβ, prophage 1, prophage 2, prophage 3,prophage 4, prophage 5, prophage 6, PPS, PKS, YVFF-YVEK, DHB andfragments thereof.
 78. The method of claim 77, wherein said alteredBacillus strain further comprises at least one mutation in a geneselected from the group consisting of degU, degQ, degS, sco4, spoIIE andoppA.
 79. The method of claim 73, wherein said protein of interest is anenzyme selected from the group consisting of proteases, cellulases,amylases, carbohydrases, lipases, isomerases, transferases, kinases, andphosphatases.
 80. The method of claim 79, wherein said enzyme is aprotease.
 81. A method for enhancing the expression of a protein ofinterest in Bacillus comprising: a) obtaining nucleic acid from at leastone Bacillus cell; b) performing transcriptome DNA array analysis onsaid nucleic acid from said Bacillus cell to identify at least one geneof interest; c) modifying said at least one gene of interest to producea DNA construct; d) introducing said DNA construct into a Bacillus hostcell to produce an altered Bacillus strain, wherein said alteredBacillus strain is capable of producing a protein of interest, underconditions such that expression of said protein of interest is enhancedas compared to the expression of said protein of interest in a Bacillusthat has not been altered.
 82. The method of claim 81, wherein saidprotein of interest is associated with at least one biochemical pathwayselected from the group consisting of amino acid biosynthetic pathwaysand biodegradative pathways.
 83. The method of claim 82, wherein saidbiodegradative pathway is disabled by transcription of said gene ofinterest.
 84. A method for enhancing the expression of a protein ofinterest in Bacillus, comprising: a) obtaining nucleic acid containingat least one gene of interest from at least one Bacillus cell; b)fragmenting said nucleic acid; c) amplifying said fragments to produce apool of amplified fragments comprising said at least one gene ofinterest; d) ligating said amplified fragments to produce a DNAconstruct; e) directly transforming said DNA construct into a Bacillushost cell to produce an altered Bacillus strain; f) culturing saidaltered Bacillus strain under conditions such that expression of saidprotein of interest is enhanced as compared to the expression of saidprotein of interest in a Bacillus that has not been altered.
 85. Themethod of claim 84, wherein said altered Bacillus strain comprisesmodified gene selected from the group consisting of prpC, sigD andtdh/kbl.
 86. An isolated nucleic acid comprising the sequence set forthin a nucleic acid sequence selected from the group consisting of SEQ IDNO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ IDNO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:39, SEQ ID NO:40, SEQ IDNO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:37, SEQ ID NO:25, SEQ ID NO:21, SEQ ID NO:50, SEQ ID NO:23, SEQ IDNO:27, SEQ ID NO:19, SEQ ID NO:31, SEQ ID NO:48, SEQ ID NO:46, SEQ IDNO:35, and SEQ ID NO:33.
 87. An isolated nucleic acid sequence encodingan amino acid, wherein said amino acid is selected from the groupconsisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8,SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ IDNO:51, SEQ ID NO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ ID NO:57, SEQ IDNO:24, SEQ ID NO:28, SEQ ID NO:20, SEQ ID NO:32, SEQ ID NO:55, SEQ IDNO:53, SEQ ID NO:36, and SEQ ID NO:34.
 88. An isolated amino acidsequence, wherein said amino acid sequence is selected from the groupconsisting of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8,SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ IDNO:51, SEQ ID NO:38, SEQ ID NO:26, SEQ ID NO:22, SEQ ID NO:57, SEQ IDNO:24, SEQ ID NO:28, SEQ ID NO:20, SEQ ID NO:32, SEQ ID NO:55, SEQ IDNO:53, SEQ ID NO:36, and SEQ ID NO:34.